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You don't need to delete your mods folder, but you will need to delete Assembly-CSharp.dll and rename Assembly-Csharp.dll.orig to that in your Managed folder and you will likely need to run Verify Integrity of game files to be in vanilla mode.
 
or like me since i got BT via steam....paradox also lets me install their version.
so i have a modded version of BT via steam
and a pure vanilla one via paradox for mulitplayer
 
That is indeed the best way to do it for MP.
 
ya if you link your steam account to your paradox account you can use the paradox launcher to install a second version of BT.