I still think he could have had flooding, gone to the bottom in a steep dive and not be destroyed. After all this is in a harbor where the bottom is well within the crush depth of the sub. As for the crashing noise, I would not put too much faith in that. Have you had the mission to insert the agent into enemy territory?

(the rubber raft sure is loud against the side of your boat). Either way, I bet it was still fun to watch that sub go down