How can have 2 different mod folders with the new Minecraft launcher?

The way I go around it is by having separate sub-folders for each profile I use in my .Minecraft directory. For example, I have a folder called 'profiles' which stores the different profile directories which can differ depending on the version or whether or not I use mods. Thus, each different profile I have in the launcher is configured to its respective directory.

For example: Say you had a Forge profile for modded Minecraft, you'd configure the Game Directory to be in .minecraft\profiles\Forge, and thus the mods folder for that would be there. Then you could have a separate folder for Vanilla or whatever (.minecraft\profiles\Vanilla) and have a different profile configured to that. You could even divide a folder in profiles further to separate different versions. The whole system is seamless.

(To configure your game directory, select your desired profile and click "Edit Profile". You should see the option to modify the directory.)