Human sexuality is extraordinarily complex and exists on a wide spectrum. There's nothing wrong with anyone engaging in any sort of sexual act as long as both people consent and are capable of consenting. You chose an extremely poor example to make your argument, though, since sexual activity in prison is very often non-consensual.
And then you proceeded to a slippery slope argument, which is not a logical sequitur, but there would technically be nothing wrong with 3 people marrying other than it would require a rewrite of the entire tax and law system and would require that polygamy was gender-neutral and power-neutral (that is, it was not the radical Mormon polygamy with a single man exercising absolute power over a number of wives). Given that polygamy is quite common in the Bible (and monogamy was a concept more commonly associated with the Hellenic and Roman world), I'm not certain why religious people would condemn this.
And there's no current group of polygamists who are ostracized, bullied, or assaulted - with good reason, as it isn't an inherent part of identity, per se, so it's not an equivalent argument, and there are good reasons the public may not support this without it coming from a bigoted place - the fundamental differences in the tax and law system would be enough. Though I also think monogamy exists because it has evolutionary roots, as well, so I don't think either system is natural or unnatural (after all, both polygamy and monogamy have appeared separately in vastly different cultures across the globe).
As for the rest of the conversation, I think, in general, it's possible to internalize an opinion or feeling without having it externalized, but there's always the possibility - what happens when you're deciding whether to give a job to a transgendered individual, for instance? I'm not sure you can put this aside. It's certainly possible this never comes up, that you never interact with a trans person at all, but this is far less likely if your prejudice is against people of a different skin color or creed. I question people who don't want to overcome their feelings of discomfort or distaste for a group of people based on something about their identity that causes no harm to anyone.
This probably came across as rambling. For that I apologize.