Hi Darthlucky,
Consider using h.sie's Realism- and gameplay-related hardcode fixes for SH3.EXE, specifically with Stiebler's add-on. IIRC, you can just get Stiebler's add on and it will incorporate the other parts. Takes some time and effort to implement, but it is well worth it.
As to your concern, Stiebler's add-on has a surrender option. In it, you are able to scuttle your u-boat and risk being picked up by your side or theirs. I seem to remember that he modeled it on the AotD idea as well.
It would certainly give you an option in the future!
Cheers!
