It's impossible to tell to what extent that is the case.
However, it is true that many religious organisations do encourage bigotry and intolerance so I don't think it's tenable to claim that they aren't behind it in a lot of cases. They often actually thrive on intolerance, both towards others and within their own organisations. Take the CofE: the Anglo-Catholic wing is where gay clergy mostly tend to be found (they have to pretend that they aren't in relationships, but it's very much a case of 'don't ask, don't tell) - but despite the discrimination which they receive, they also dole it out and it's the Anglo-Catholic wing which is most opposed to female clergy. Don't ask, don't tell isn't an option here, so the CofE, of course, panders to that bigotry by having a system where the most deeply misogynist churches can choose to report to one of the 'Provincial Episcopal Visitors', who are basically bishops who exist solely to avoid such churches having to report to a bishop who has ordained women (and indeed may be a woman now, but that wasn't the case when this system was set up). I can think of no secular eequivalent where gay people would have to pretend not to be in a relationship, or where such an elaborate system would be set up in order to pander to misogynist bigotry - both of these scenarious would be considered completely unacceptable in any non-religious organisation.
Nope, sorry, not going to accept that this is a valid argument. Western society has moved on and homophobic attitudes are no longer regarded as acceptable, just as racist attitudes aren't, and anyone displaying these attitudes is a bigot. Likewise, the anti-women attitude of various religious organisations is equally unacceptable, and is also bigotry.
There is no 'reasoned debate' to be had on the issue of homosexuality - it's one of those things, like race, which are part of who someone is (it's how they are born) and there is absolutely nothing to debate.
The test is whether any views would be regarded as unnacceptable and bigoted if there was no religious justification behind them. And in all the above cases, that would certainly be the case.