Allowing this so called "Church or place of worship/mosque" would be similar to allowing Headquarters for the KKK in the middle of Harlem.
Nonsense. A similar analogy to yours is to say that no churches should be built in Harlem, because the KKK were Christians ( and used the Bible and their Churches to support their anti-black beliefs); therefore all Churches are offensive to blacks.
The people that attacked the United States practiced a twisted form of Islam, just like the KKK practiced a twisted form of Christianity.
I don't agree with the mosque for many of the same reasons as the moderate Muslims described in the Boston Globe article; however, your analogy is way off.