You have three options:
Option #1:
The Mod Launcher will keep you up to date, and over-write any changes you make. However, you can disable the Refresh Mods Automatically, and make all your changes in the "TempMods" folder instead. This will make more sense when you install the mod.
Option #2:
You could use the Mod Launcher once, to create the folder, download and install the game (needs to hit Play once). Then make your changes as you normally would, and just launch 7daystodie.exe in the new folder, rather than using the Mod Launcher.
Option #3: (more advanced)
Edit the XML that you normally do to remove the bears. Then host the file somewhere, like pastebin.com (never expire). We can than make you a personal configuration, that only you see, that will keep all your files up to date with dwallorde puts out, but your change in that other file will overwrite his, every time. So if you remove the entries in entityclasses.xml, you'll use your own entityclasses.xml, but all his other files. This would be using the "My Mod" functionality in the launcher.
For the steam controller, I'd recommend adding the 7d2dmodlauncher.exe to steam, as a non-steam game. Then, launch Steam in Big Picture mod, and start the Mod Launcher. Your modded games will use your Steam controller (wife uses one).