I think making these functions return -1 when bUseMediaEngine is off should essentially disable it:

sceMpegInit
sceMpegCreate
sceMpegAvcDecode
sceMpegAvcDecodeYCbCr

Although, it may be better to fix the problems.  For example, jumping to the debugger I found that Holy Invasion of Privacy is hanging because it expects # packets to be a hardcoded number that is higher than the one we currently calculate, afaict.  I haven't tried messing with the number or calculation.

-[Unknown]