I dont know if it is possible. Is the game via Steam? If so then probably not. I guess you could create a second Steam account with a seperate install, but that would mean buying the game again.
Could you create another user account on your PC, and try installing it there, ensuring that each install is only available to that user. Should give you two independant installs, but you may be tripped up on the serial number.
Might be worth a try anyway!
I thought it was just mods which gave you an unfair advantage that mean you couldnt do online with them installed (as opposed to just visually enhancing mods) and in my opinion, there isnt any point in using sticky kerbs, or 500 flashbacks in any game mode.
I would say to use the RD mod manager (lets you enable/diable mod very easily) but I had a go with that last night and im rather embarrassed to say I couldnt fathom it out when trying to install the truelight mod with it, so I painstakingly had to replace each file!