I have seen a yacht club rescue RIB transom crudely built up with timber to prevent this. I guess you could build up the transom either side of the engine. (Mine has a sort of "notch" where the engine is fitted and rises up to where the tubes are.)
I am guessing the "pooping" effect is from waves whilst stationary & diving? You are not getting swamped by your own wash are you? If so the don't slow down so suddenly
!
Apart from that, fit the biggest electric bilge pump you can to clear the water as fast as possible!
Cheers,
Alan