to be fair, I haven't actually played the game in a while, but I think you are reading a lot into alyx that isn't really there. I don't remember having the impression that alyx was in love with Gordon or really picking up on any sexual tension at all.
(tbh I only skimmed them right now .. and I unhearthed them with the totally biased "alyx bad character" web search, although I remember reading the second link when it came out)
I read the first article you linked. I guess I was really oblivious as a teenager; I just thought of alyx as a more convincing friend than most video game sidekicks. as an aside, I don't think all the screenshots with 3rd party alyx models were necessary to make the point.