I still don't have a fix for this, though I've looked long and hard for something that would work.
I have, however started to grow accustomed to using the keyboard shortcuts for things instead of the mouse.
Where i was used to clicking to get my cursor back, I hit F1 instead (to bring it back when needed)
Instead of clicking the red launch torp button, i use the shortcut ctrl-enter and the 'y' key to cycle tubes.
Depth control, direction and speed I now all control with the keyboard as well.
I'm starting to adapt to all this from being a mouse using click happy s.o.b but I would still love to find a way to fix this problem. Sometimes while peering out my scope if something startles me I twitch and click and ah damn there goes a torp.
I'm almost considering posting this in the SHIV area just for extra exposure. :-/