Real subs didn't automatically broach if stopped. It was trim dependent, but trim varis from moment to moment, someone walks from one part to another of the sub, the water temp changes, etc, ad naseum. Unfortunately, the two solutions to hack this behavior into SH3 don't seem to work in SH4 (making the sub slowly surface all the time without down-planing, or having it slowly sinking without up-planing).
The simple solution for the gamer is to not stop the sub, or only rarely and for a very short time period, and never shoot while stopped. Easy enough to not cheat, really