I would actually argue that while FSA has a reasonable incentive to run away (I assume you are referring to the BL shift from losing ships/squadrons) it is not all that easy to run away in the game. I think you would see a lot more of it if players didn't have to spend two full turns to get models off the table via FSD. Look at BFG; all you had to do to get a ship off the table was to pass a leadership check. If you did, you could take the model off the table immediately. BFG also gave you the option to disengage by driving off the table edge; this counts as a destroyed result in FSA. Now, disengaging like this isn't free (it is 10% VP to your opponent for ships with more than half HP, 25% for ships with half HP or lower), but it was much easier to accomplish and didn't require telegraphing your intentions to your opponents the way FSD shunt out does. I think that your best bet for injecting a healthier regard for force preservation is a campaign setting that penalizes the losses of a ship; when I'm playing a one-off game, it's tough to worry too much about losses. Scenarios can help with this, though not to the same extent as a campaign.
Convoy tactics and convoy practice could be two very different things. Speaking in terms of the WWII Battle of the Atlantic, at first the tactic was to have a ship towards the rear of the formation stop to assist a disabled ship. In practice, this was rarely done, as it made the ship that stopped to assist the damaged one a sitting duck, and stopping was left to the discretion of the skippers of the merchant vessels in the convoy. The convoy escort commander could also detach one of the escorts to aid a stricken ship, but this was uncommonly done due to the fact that for much of the war escort vessels were in very short supply. Some convoys only had a single escort vessel for the whole convoy of 20 or 30 merchants, and if that escort stopped to help one ship it left the rest of the convoy vulnerable. Eventually, specialized rescue ships began to be sent out with convoys. Their job was to rescue the crews off of ships that were sunk by U-boats, and were equipped with additional medical capabilities, small boats, etc. They had a shallow draft, to hopefully reduce their vulnerability to torpedo attack. As one might expect, the merchant sailors loved having one of these ships in their convoy, but just like escorts they were always in short supply. Only about 1 in 4 convoys ever sailed with a rescue ship in company.
I have seen various attempts to incorporate Convoy battles into miniature games, for example the BFG has a Convoy scenario included, which I think is half-way decent. This is a difficult aspect of naval warfare to capture well with a miniature game. In real life, the convoy could be attacked at any time. In a minis game, you know you are going to be attacked in the next 2-3 turns, because you are playing a game with an opponent!
