The most negative point is genny ground, so the caps are the right way around.  It would have clearer had I posted all the circuit.  It's here.  I've tried adding diodes but the LTSpice model never shows anything but a few microamps going thru the diode.  The real circuit may be different.  I like your idea of adding a diode going back to battery +.  It should limit voltage at the fets to whatever the genny produces plus the drop across the diodes.