The main reason I'm skeptical is that Elo is a system designed for two-player games, and Breakaway is a 3v3 game. In addition, Elo is based on a very important assumption: that performance can't be measured absolutely; it can only be inferred from wins, losses and draws. By its very nature, it doesn't take into account the score of the game, or anything other than wins and losses. For chess, this is fine, as there is no metric of showing the strength of a win, but in Breakaway there is one so not using it will only produce a ranking system that turns out results similar to the finals.
Elo would be better in my opinion for ranking alliances, and then I would rather look at things like score differentials, etc. to determine relative strength of alliances in a somewhat objective manner. I am far from an expert on ranking systems, though, and if I'm wrong I'd love to hear why.
