So the solution to my problem is to strike the -fno-mco flag on bdepend, and add a -fmco flag when bigloo is compiling a module. Ta-da! No more inconsistent module initialization, and no more complete system recompiles. Wonderful!
P.S.--Maybe someone (me?) should write something up for inclusion into the Bigloo manual about bdepend and mco files. There's very little in there right now (hence my problems making this work).