Sure, it could be about a gay couple, but it also could be about a straight couple where one partner is considerably older than the other, or one of them is of another ethnicity etc., the possibilities are endless. I live in a small village and if I turned up with a boyfriend who was merely a tad unconventional people would give me strange looks and talk about me for weeks. It wouldn't be any different if a gay couple walked down the street. Same with The Boy With The Thorn In His Side and Hand In Glove, I'm not dismissing the idea that these songs could have a gay theme, but they could as well be about two outsiders.
Also, to address some other posts, it's also possible to feel unloved and isolated if you're, say, extremely shy and have no self-confidence. That's just an example, there's a sheer endless number of reasons why somebody could feel this way. It's not an exclusively gay thing. Everybody will read into a song what's closest to them.