We should be able to set the type of each team on the server:
team 1 aliens
team 2 humans
team 3 aliens
...
For starters:
Right now, if you spawn as a human in the alien team, by editing sg_cmds.cpp:
newClass = PCL_HUMAN_NAKED;
the alien defense structures start attacking you, altough you are on the alien team, and only changed your class to a human one. So i guess there is a lot of things hardcoded to react on the class instead of the team.