They did. Their fight and priority was to destroy as much classified material as possible. The Captain used delay tactics to try and buy more time. Their sole defense was a 50 caliber on a ship that was supposed to be unarmed to start with.
There wasn't much else they could do. They were burning material which was priority number one and busting equipment but only had one incinerator. They were using waste cans for burns as well. If you don't have the means to fight and you have classified material you as quickly as possible destroy the equipment. They had no explosives nothing to work with despite the Captain's request and expressed concerns for such. Scuttling the ship was impossible as the Navy builds ships to resist sinking.
This wasn't a field combat nor a typical Naval attack. Now had it been a carrier coming under attack and in danger of capture or being over ran by the enemy? There would have been a different outcome. 5000 dead squids and a ship on the ocean floor.
At least they should have sent them out with a ship better equipped to get rid of all the intel gear, and maybe one for easier scuttling if needed.