You can run the game without the .minecraft folder it won't run as far as I know, what you can do is make backups of different setups and different mods and just switch thru them using bat file or manually renaming them so
.minecraft1 will have mods for server A
.minecraft2 will have all the mods for Server B
and .minecraft will be the current setup used and with settings setup to play on server C
I know Tekkit has some Launcher that would switch folders for you, but for the love of myself I haven't been able to install it and have no time finding out why.