A lot of ancient civilisations or even more recent ones have vivid histories of Homosexuality.
A lot don't as well.
Pink also use to be quite a manly colour, even 500 years ago or so.
So really, as times change, different things become taboo or strange. Some become entrenched in the minds of others and with the ease of communication nowadays, it can be quite easy to be influenced to believe something whilst at the same time, it also is quite easy to diregard other beliefs.
Completely off topic there probably but the way I see religion in Freelancer would be this.
Christianity would most likely have gone down the current route it is going, with many people turning more towards other beliefs (including atheism, scientific logic things etc) but with the long war, people may have turned more to religion than ever.
A thing to remember is that it was mainly Westernised countries that made up the Alliance and hence the origins of the Sirius colonists. Religious freedom is something many of those countries are striving to maintain.
If you want a religion in Freelancer, use one other than the mainstream ones today. Whilst it may be realistic to use the current ones, it would bring an extremely volitile element into the mod that it really can do without.