Let's imagine a scenario with a real life MMO. To make it more realistic, let's say there are all guys and 1 girl.
The people in this MMO play together in the same guild because they're friends and have fun. Then the girl hooks up with one of the guys. Are all of the other guys just going to quit the guild even though they're having a good time? Most likely not. They'll still hang out, and probably continue to talk to and flirt with the girl a little even.
Heck, when I played WoW, our 40 man raiding group had a couple women. One was even married with her husband also in the guild, yet she still talked to everyone a lot and made jokes and stuff with everybody.
I don't think this situation is really that far from what is presented in SAO. The unnatural part, of course, is that the male to female ratio is reversed.
As for your endgame thoughts, some of them are questionable.
The only reason Shino played GGO specifically was to get over her gun issue. If she can have just as much fun with any other game while also playing with friends, why wouldn't she do that? Although she got over her gun trauma, she probably has new male/relationship trauma that she needs to get over.
Suguha is way too young for Klein. Like, seriously. Maybe if they hung out and 4-5 years passed and they were still interested, maybe...
If anyone, I think Liz gets along best with Klein. Still pretty young, though. Klein's like 8 years older than them (and Sugu is younger than Kirito).
Which brings us to your last point. Poor Liz... What's wrong with Liz? I don't think she deserves to be forever alone. She needs to get over Kirito, though.
Sugu actually already has a potential pairing in that random kid from her school who she doesn't really hate or anything. She just has major oniichan problems.
I think the most awkward part of the whole SAO harem situation is that Kirito and Asuna got married in-game, but not in real life. Kirito also has no idea how to handle all of these women coming onto him when he really has already decided.