SH3 is a great pick.. I bought a copy in late July, through Amazon, for $16 with shipping. Easily the best $16 I've spent in a while, and after modding it with GWX and Sub Commander.....it's immersive as hell. Enjoy SH4, and when you're ready to play a little cat and mouse in the North Atlantic, jump right in with SH3!!
BTW -- Don't feel bad about sinking Allied merchants or warships. Given the chance, they'll gladly do the same to you.
-FF