Well, the issue as I see it is that, at the moment, retreating does two different things, but they aren't in-game well distinguished.
1: it gets an injured ship out of combat (tactical retreat)
2: it gets the entire force (when appropriate) out of the battle (strategic retreat)
What I might suggest is to have those a bit more differentiated. One way it could work:
A: If you are escaping, it works as normal.
B: If you aren't escaping, ships that retreat are returned to your pool of reinforcements.
B1: If your enemy was defending or escaping, and you have no ships on the board, you are free to declare a strategic retreat - you can get away clean; no damage, no capture chance, etc.
B2: If your enemy was attacking, and you have no ships on the board, bad things happen - ships take damage, lose crew, get captured, etc. (Probably to a greater degree if you attacked than if you defended, though.
Combine that with, say, a FP bonus for defending or escaping, and suddenly you've got good reason to actually use all three options. You attack if you don't want to let the enemy get away and are sure you can win. You defend if it's a more even fight and you're willing to let the enemy escape if it means better odds in the battle - this option also means you can still retreat damaged ships off the near edges of the map. And you escape if you, y'know, want to actually escape.