If you're trying to integrate crippling into the game, why not have battlefield effects that last until the engagement ends, that is to say, until you withdraw or retreat from a fight to the overland (reploying against the same enemy still has the effect). For example, if a ship gets alpha striked for more than 50% of its health on its engines, the engines continuously malfunction for the rest of the fight regardless of CR, or have a more unique effect, like manuvering is 50% disabled on one side. If they get alpha striked on the front, their targeting systems go crazy, with 100% more recoil, or their shields randomly vent when struck above 50% flux. Things like that.
The problem with crippling effects that require station repair is that it doesn't really change the game all that much. After a fight where you get mauled, you have two options - go to a station or wait until you auto-repair. With crippling, you eliminate auto-repair. I don't see the point...
One thing you could do is tag ships with the inability to travel near stars, or enter wormholes, or through asteroid fields, without risk, if they've been "overland" crippled. That would change the game in a semi-meaningful way and perhaps limit your options of escape if you're running from an enemy fleet, do I dump the dud ship, or jump, or retreat away from stations but towards safety...meh