I've been trying like hell to eradicate some message boxes from a few mods only to find out they've more than likely been scripted. Without access to the source, is there any way, on the user side, to disable the appearance of debug message boxes?

Well, that was easy. All I had to do was comment out the function (and the call to that function from the TraceAndBox function) from debug.psc and recompile. BOOMSHAKALAKA!