Now of course this problem does not exist on the rotation server, as teams are scrambled with every map change. Hell, if the server was actually mildly popular, I'd play on it more, but that's another story.
What I propose is that the server "restarts" the map, in a similar way to a map switch, when a score limit, 5-10 would be perfect, is reached. That way it keeps the players shuffled, preventing steam rolls or stacked teams to a certain degree. I'm not aware if that is possible, however I request that you look into implementing it Bottiger :)
Now I know this isn't the perfect solution, and not everyone will be happy. However friends who want to play on the same team can probably communicate that among themselves through steam chat or something. I'm aware donators can still switch teams regardless, however I trust the judgement of people who have given money for these servers, no not fuck it up. Also, people with 1k points will just have to suck it up I guess.
TL;DR stacked teams are for noobs who are too pussy to play in balanced ones, so restart the goddamn map.