Uhh, I'm pretty sure this exact mechanic is the game saying you can repel the attackers without incurring reputation penalties.
Every single individual engagement you have in the defense of your colony incurs a 3 point penalty, the last time I got attacked the Perseans sent what must have been at least five fleets, and they seem to be attacking that colony at least three times a year. At this point they're pretty far beyond ever gaining favor with but it's still obnoxious. Sure I
could go raid all their markets until they destabilize and just wipe the faction out entirely, but just killing all the other factions is a nice way to end up with a boring sector where nothing happens except pirate and pather bounties. Having to drop what you're doing to respond to an attack or potentially suffer the consequences of a raid should be penalty enough for contesting their market shares, not an endless stream of suicides that inevitably leads to a state of permanent hostilities.
I just reinforced a defense and only got a rep hit for running down the defeated fleet. I don't think you're getting a rep hit for defending yourself, you're getting a rep hit for murdering the merchant fleet supporting the (defeated) military raid. I think if you let the backliners run home w/o incident you don't get any hit
If vaping the poor sods in a retreat is what sets off the rep hit then that's still a problem, because when you get a warning that your system is under attack then the natural response is "well I better go break out the big guns then". But if you try to intercept the raider fleets with a big fleet of your own, they will always run away from you, which means any engagement you force with them will be a pursuit that drags the logistics ships into the fight. So what am I supposed to do then if killing the logistics ships is the problem? Bring a smaller fleet so they don't run away and up ganked by the four other task forces joining the battle when I make contact? Stand around and wait for them to engage the battlestation or my patrols? Neither option sounds fun. Besides:
Persean League Task Force attacks my station (after the popup has already listed the raid as "Defeated", mind you), I go to assist.
The Perseans are defeated, no pursuit is given, -3 rep.
Tritachyon raiders are engaged with my patrols, I go to assist.
The Tritachs are defeated, no pursuit is given, -3 rep.