Hmm, strange one that one. I've heard many people say that they've successfully sunk the carrier inside the port without experiencing a CTD. Try a previous save to the one you are using. What mods are you using, could there be a conflict? Sinking the ship might not be the sole reason for CTD. I often had CTD's returning to base, these in hindsight were due to mods.
Note that sinking a ship in port can often not count towards your mission objectives, so my suggestion is to ignore that ship and try to catch a carrier in open seas. Anyway, It's not realistic, in reality the ship would of been heavily defended - wire, mines, etc.
You should check the temperature of your motherboard and graphic card. Whenever I shoot a torpedo in a heavy environment (i.e.: a port, a big convoy and so on), my graphic card gets overstressed and may throw me out of the game.
Same on this end - Steam version (1.2), German data folder.
I sink the Ark Royal in Plymouth harbour and my XO begins informing me "Capital Ship, bearing ***. Short range." This goes on for about a minute or two (he lets me know about the phantom capship about every 10 seconds) and then with no warnings or error messages it crashes to desktop.
Temps on CPU & GPU never go above what I usually see when they're taxed, and the game runs perfectly fine in all other respects - so I think it's just one of those bugs...
I have been getting this problem too on Blockade of Germany I cant for the love of god find a carrier task force out at sea but I have found the ark royal at Plymouth but it crashes about 20 seconds after i sink it. It has nothing to do with graphics my pc is very powerful and can handle much more. I would love to keep playing this game too.