but that's always just been a plot device - who says the only identity of high elves is that they're not horde?
there seems to be some clear ideological and philosophical differences between the two groups a creative developer could easily expand on or emphasize to show the two are different. They have different views on the magic for one - high elves believe in balance and harmony, blood elves believe in power and using or doing whatever it takes to survive, use to be power at all costs, but they've softend from that.
Also there are other ways you can make them more distinct aside from being on the other faction. Eye colour is one, but also colour themes - the blue and silver versus red and gold, you can even have Silvermoon have a blue half and a red half, have high elf villages and blood elf ones so they are presented as two sides of the same race. And yes, high elves could be friendly with the alliance even if players cannot play with them on the alliance, whiles blood elves fully horde, if they made high elves playable on the horde, it would be something like a high elf project to reach out to their blood elven kin to help them. or whatever excuse.. you don't have to have all the high elves on the horde either as has been said earlier. You can have some still on the alliance only, whiles this other group, alliance friendly helps out the horde.
it's all in the story, it's quite possible i feel and would be good too, I feel also.