I think, a copy (with little corrections and additions) of an extremely biased oversensationalistic research isn't a research. It also looks like the OP didn't even try to check the facts and conclusions and to add notes and references despite he had 2½ years to do so.
On the merits:
Since the conviction of Rutherford and others was reversed and annulled, and charges against them were dismissed on May 5, 1920 by federal judge on motion of US attorney Leroy W. Ross , they were, under presumption of innocence, legally not guilty and didn't need to be acquitted.
There are also different ways to interpret the Circuit Court's decision (available here, p. 100-107). For example, that the incident with Hudgings and two other witnesses was used as a pretext, the simplest way for the Court to reverse the conviction that could be deemed unjust or too harsh  — and was possible only during the wartime hysteria  and “spy mania”  — and to avoid deciding on the issues of whether the trial was fair  and whether the punishment was too severe. This is a common judicial tactic; compare the IBSA case with the Masterpiece Cakeshop one.
Don't also forget that the DOJ “reviewed the sentence of nearly every Espionage and Sedition Act prisoner who was sentenced to more than a year in prison, and a few sentences of those who were sentenced to less than a year.”
John Lord O'Brian, the chief of the Justice Department's War Emergency Division, and Alfred Bettman, who served in that division under O'Brian, examined a large number of the Espionage and Sedition Act convictions from all across the nation, and recommended pardons or commuted sentences in what they saw as deserving cases. In 1919, these two officials secured pardons for 200 people (…) Additionally, between 1919 and 1924 many of those convicted had their sentences commuted, which showed that the government considered them much less a threat once the war was over (…) in June 1924 the last inmate held under the Espionage and Sedition Acts was released from a federal prison 
For example, a preacher in Vermont sentenced by Judge Howe in March 1918 to 15 years in prison was pardoned by President Wilson and spent only one year behind bars . More specifically, Judge Howe “has written to the Attorney General, urging the sentences [of Rutherford and others] be commuted”. So, unless you have carefully examined the possibility of reversal of the conviction on other grounds and of securing pardon in 1919 (or subsequent years), you cannot certainly conclude on the real impact of the testimonies of Hudgings and others.
As to Joshua “Jehovah” Sykes, it should be noted that we have little information about him and his church — no recorded sermons, no printed publications, and probably only one academic paper . AFAIC, the only primary sources are multiple newspaper reports, criminal trial files (brief description of indictment against Sykes is available here) and few documents from ACLU archives.
In addition to lack of information about Sykes and his followers, I want also to note that no proofs of any connection between Sykes and Rutherford and any influence of the former on the org were presented.
It is interesting also to compare different accounts on the 1926 case provided by ACLU. Elmer Clarence May wrote, citing Roger Baldwin’s letter to Carl Whitehead (April 24, 1926, ACLU Archives, vol 299, "Colorado."):
The Jehovites, or "children of Israel" were a small sect of approximately six hundred members, concentrated in the area around Denver, Colorado and held together by the strong personality of their leader, "Joshua Jehovah." The Jehovites viewed flag exercises and other ceremonies as idolatrous and hence opposed participation in such exercises. Although the flag exercise ceremony had been used only infrequently in the Denver public schools, in 1926, the Jehovites announced that their children would refuse to give the salute. The school board told at least twelve Jehovite students to salute or stay home. By April of 1926, fifty Jehovite children were out of school. In the fall of 1926, after the dominant school board figure had moved away, the Jehovite children enrolled in school without incident” .
According to ACLU brochure “Free speech in 1926”, the expelled children “were readmitted, however, when their parents put aside their religious scruples against recognizing “earthly courts” and showed a disposition to contest the ruling of the board” (p. 21-22). Finally, according to 1931 brochure (p. 13) “the religion of the Jehovites does not recognize earthly courts, and consequently the parents refused to take legal action, as attorneys for the American Civil Liberties Union advised. Negotiations finally brought the school authorities around, and they allowed the children to return to school without requiring them to join in the patriotic exercises.” No major contradictions, but it would be interesting to know certainly and in details what happened in Denver in 1926.
 NINE RUSSELLITES GO FREE. Eight Had Served Part of 20-Year Espionage Sentences. New York Times; May 6, 1920. P. 6.
 For example, "[w]hile denying that the Department [of Justice] had prosecuted people solely on the basis of their ideology, [US Attorney General Thomas W.] Gregory entertained the possibility that some people had perhaps been unfairly punished [in its February 1919 circular to US attorneys]: “...it may be that during the war some individuals in close cases have been convicted upon inadequate evidence of their wilful intent to interfere with the war program, and others have undoubtedly received sentences unduly severe” (Wiiliam H. Thomas Jr. (2002). The United States Department of Justice and dissent during the First World War. Ph.D. thesis, University of Iowa. P. 220-221).
 For example, Justice Oliver Wendell Holmes wrote to Harold Laski in March 1919: “The federal judges seem to me (again between ourselves) to have got hysterical about the war. I should think the President when he gets through with his present amusements might do some pardoning.”
 John Lord O'Brian (1919). Civil liberty in war time. P. 5.
 On the possible procedural shortcoming and the judge's bias see: Lon J. Strauss (2012). A Paranoid State: The American Public, Military Surveillance and the Espionage Act of 1917. Ph.D. thesis, University of Kansas. P. 105-111.
 Scott A. Merriman (2003). Ordinary people in extraordinary times?: Defendants, attorneys, and the federal government's policy under the Espionage and Sedition Acts during World War I in the Sixth Circuit Court of Appeals district. Ph.D. thesis, University of Kentucky. P. 388.
 Ibid. P. 17-19.
 Gene Sessions (1993). Espionage in Windsor: Clarence H. Waldron and Patriotism in World War I. P. 149-150 [18-19].
 APPEALS FOR RUSSELLITES. 20-Year Espionage Sentences Too Severe, Says Federal Judge. The Washington Post; Mar 16, 1919. P. 17.
 Johnson, A. S. (2016). A Shudder Swept Through Them. Pneuma, 38(3), 312–329. doi:10.1163/15700747-03803002. Funny quote: “By 1920 many church members had changed their last names to Jehovah. The 1920 Denver directory listed over sixty households with the Jehovah name. (...) By 1925, there were over one hundred Jehovah households” (p. 326). Read also a journalist article on the subject: https://denverite.com/2016/12/14/joshua-sykes-colorado-cult/
 Elmer C. May
(1995). An investigation of the relationship between the First Amendment to the
United States Constitution and public school patriotic expression (freedom of),
policy and practice. Ph.D thesis, George Mason University. P. 122