How about a CL program that explicitly sets the classpath and then calls your RPG program?
The CLP:
PGM
ADDENVVAR ENVVAR('CLASSPATH') VALUE('.:/dir1:/dirA/dirB:/javaToolkit/jt400.jar') LEVEL(*JOB)
CALL PGM(MYLIB/MYPGM)
ENDPGM
This page may also be helpful.