That wouldn’t be a bad idea, it’s actually been suggested before here:
Matchmaking isn’t perfect, as you’ve pointed out – only the top 30 heroes of all players are accounted for. This is usually good enough for alliances with lots of players. But that means small alliances (such as yours) gets more bad matchups from time to time – there’s also less alliances to be matched up with, which makes the matchmaking problem even more complicated.
Unfortunately, I doubt more work on wars is going to come anytime soon. I think the developers consider the matchmaking to be good enough, and they’re clearly working on other stuff to deliver for next year (based on announcements we’ve been getting).