Indeed. Personally, I'd rather see a non team colour image than one that wouldn't be able to have AA.
Another idea (abet, more complex, but solves the AA problem):
Use a monochrome image where pure black = full transparency, while pure white = full teamcolor (opaque). Thus, greys could cause AA. No way to set explicitly how dark or how light the team color should be, though you can specify the how transparent the part is, which gives the illusion of volume. This should be possible, as I've seen other games do it, as well, it's a very common method for terrain rendering. Probably very complex to code though.