I didn't have the time yet to make two config files and would have to read up about the scripting to do the automatic swap. This one is the only situation where I would use a different bind for the button. I don't play that much so it's OK 
All you have to do is duplicate your autogen.cfg file twice and rename the copies to aliens.cfg and humans.cfg, like I do.
Also, there's no complex scripting involved in swapping configurations; I simply have mine as follows:
bind h "team humans; exec humans.cfg"
bind j "team aliens; exec aliens.cfg"
bind z "team spectators; exec autogen.cfg"
Using separate configuration files lets you have custom binds specific to one team. Example; my aliens.cfg file contains the upper 0-8 keys as evolutions. 0 is granger/advanced granger, 1 is dretch, etc. Once humans.cfg is executed, however, the 0-9 keys become weapon binds. 0 is ckit/advanced ckit, 1 is rifle, etc.
Once you get basic knowledge of binding things (check out the wiki on
www.mercenariesguild.net) you can do so many things with it, it can sometimes be overwhelming how you think so fast and type so slow.
EDIT:
Here's the direct link to the comprehensive MG guide on binding;
http://www.mercenariesguild.net/component/option,com_openwiki/Itemid,12/id,binds/lang,en/Read it and you'll see how easy it is to make yourself look uber-leet with custom binds.