You guys are weird. AU!Charlie wasn't checking if our Charlie was gay - she was trying to work out just how wary of Dean she should be. Say Charlie was Dean's dead wife - wouldn't Dean think he could cross into a parallel dimension and force this Charlie to replace her? Or maybe she broke his heart - that would make him violent? AU!Charlie doesn't trust Dean, and that's normal. For a parallel storyline, see The Magicians (AU!Penny and Alice).
I think those are also plausible interpretations. I don’t actually see why she couldn’t have been doing both things though. She’s canny, wary, having lived in a world in constant war. Of course she is checking to see if Dean and Ketch are friends or foes. They did rescue her but for all she knows they may have rescued her only to use her to for something else, as you point out. She’s a leader and a tactician and she need to suss out this new information.
But when a clear point is made in the dialogue about what precisely the nature of their relationship in Dean’s world was, and Dean explicitly tells her and the audience that they were sibling-types and that his Charlie likes girls, why assume that it has no significance? It’s Occam’s razor for me. If it takes more effort for me to see how a conversation would have no implications about sexuality than it is to say that it might, well, why do the harder thing? Especially since dialogue can perform multiple kinds of work at once: doing some exposition, surfacing some themes, building a character. Your reading sits fine with those that think the writers were making a point about sexuality.
But even if it didn’t…that’s ok. There will always be a multiplicity of interpretations of this and any text. You might find it “weird” but that’s allowed, right? We can all come across various interpretations we find weird and just shrug and go “not my thing.” I hope we can all be generous that way, letting other people think what they think and express those thoughts on their personal blogs without feeling the need to prove that they are WRONG. A non-anonymous engagement with arguments, interpretation, and evidence is fine and many people enjoy that. But there’s no cause to try to make people feel bad or stupid for reading something a particular way.
I’m assuming maybe you didn’t actually mean to seem rude or hostile in saying “you guys are weird because you don’t think what I think” but it does come off that way. No one of us has a monopoly on interpretation–not any of the meta writers and not any of the folks who disagree with them. Personally, I’d be really sad if interpretation were singular and something that you could just resolve and then leave, y’know? My hope is that we can all just to live and let live, engaging in open and respectful dialogue if you want and just scrolling by if you don’t. Let’s not forget that we came here for fun! I hope you are having fun with this new season too.