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To add to the above, the Imperial Creed is noted for its adaptability, it's said to be quite easy for the Ecclesiarchy to "apply" it to a wide range of cultures. If I recall correctly, an example given is that the Ecclesiarchy would be fine with a more feral culture where they still do human sacrifice, as long as the sacrificing was done in the Emperor's name. Given this flexibility, I think it's quite plausible that homosexual/trans people can co-exist with the Imperium's religious side.

Don't expect GW to outright say it, mind you. They do tend to stay away from sexual and romantic type stuff, so "it's most likely tolerated or accepted in places" is probably the best answer anyone can give. However, if you don't mind using BL books in your view of the setting, a few examples can be found there. I'm told that an Abnett book (a Gaunt's Ghosts one, I think) had a homosexual male couple which the protagonist doesn't seem phased by, and the Cain books have two lesbian guardswomen. Don't know if trans people have ever been mentioned.

 Andilus Greatsword wrote:
I believe there was a lesbian couple in A Thousand Sons if I remember correctly, and they weren't looked at any differently. Obviously that was M31 so things are different now, but I imagine it's like the users above had said.

The lesbian couple in Cain are portrayed well too, and that's in M41. They're both good soldiers, and their relationship even helps them pull through the horrors of a Necron tomb.

But of course, this is assuming a consistency between BL authors, which often isn't true. But I like to think that both examples are valid when put alongside the GW stuff, myself.

 Dark Apostle 666 wrote:
I seem to remember reading somewhere that gay relationships are against regulations in the Navy - though that might be only in the case of a cross-rank relationship, and the possibility of nepotism, rather than anti-homosexual laws.

I'd imagine that romantic relations of any kind within the ranks would be disallowed in most of the Imperium's armed forces.

 Lynata wrote:
*shiver* Redemption Corps .. that novel where a Stormtrooper is shooting his way through an entire convent of Battle Sisters. ;p

Who are knowingly serving a radical Inquisitor, no less.

Even when I read that as a kid, and had no particular interest in the Sisters, I still thought that their portrayal in that book felt weird.

Actually, I should clarify, I enjoyed Redemption Corps too, when I read it. The action was fun, the rivalry between the protagonist and the Commissar in training was interesting, and genestealer infected Orks were good antagonists. Its portrayal of Sisters is probably the one thing I dislike about it, but apart from that, enjoyable book.

As for the Cain novels, I got the impression that the examples of squad relations we see there are allowed to carry on, in part, be due to Cain's unusually liberal attitude. Normally it's the Commissar's job to root that stuff out, yet he's quite clearly not inclined to do so. I mean, some of them are implied to have made babies, yet Cain maintains his rapport with the troops and is still said not have executed anybody. If a proper Commissar was assigned to that regiment, things like that would most likely be violently rooted out and punished.

But, as you mentioned, a healthy dose of salt is probably nedded for some aspects of the Cain novels regardless.