To disable the B-Team Mod you must not delete the .pro files but the following scripts from the data\scripts: dcvic.int, gclenny.int, kcsulik.int, mcdavin.int, mcmiria.int, nhmyron.int and vccasidy.int.
Yes, the weapon thing is a bit annoying. :(
Do as you wish with the patch000.dat file. :)