There are two aspects to the problem I can see.
The first is how one interprets homophobia. For some, simply disagreeing with homosexuality (as the Bible does) constitutes homophobia whereas for others the margins are broader. Does disagreeing with Islam make one an Islamaphobe? Does disagreeing with Christianity make one a Chrisianphobe (does that word even exist???)?
You might argue that an individual's sexuality cannot be treated in the same way as something like religion or a political view but then you have to ask what about the view of hetrosexual adultery or fornication. Witnesses disagree with this as well - does their public condemnation of this in itself constitute some kind of phobia or hate speech?
The second aspect is tolerance. It's quite possible to disagree with a religious or political view yet tolerate, respect or even be friends with someone who holds a view different to yours.
Witnesses would argue that they tolerate gay people just as much as they tolerate anyone else outside of their organisation. They would claim that a gay person can become a Witness. They would use that as an argument to suggest they are not homophobic.
The problem is that the club rules do not permit a gay person to lead a fulfilled and open life and be a member of the club. Is this homophobia or yet another case of the balancing act that humanity has to undergo to try and square the circle of free speech, free thought, tolerance, acceptance, equal rights and so on?