Various ways to do it... either a modified version of the pr.exe or just remove the warning screen from the testing/development version. I think there may be a pr_r.exe or something floating around, maybe a current dev can pitch in?
guys, how pr.exe is interacting with bf2.exe? does it hooks bf2.exe process or what? if so - you could make a dll instead of an executable. that way ppl would be able to run bf2.exe and have shaders. one headache less