I think this is a case where a combat player used the strategy of purposely underfitting an FSD once in system so they can eek out an extra few m/s due to lower mass. This was no accident, or ignorance. This was purposely done knowing full well what the risks were. That is a different issue than the punishment mechanic. I would be fine if a commander couldn't get out of the system due to their outfitting, that a self destruct put them in a detention center in a starting sidewinder with no option for rebuy. That way they aren't stuck, but also learn a very important lesson...sort of like the shieldless trader that get blown up with 50 million in cargo.
I put the inadequately installed FSD right up there with flying without having the funds for insurance. Both are done with a conscious decision by the Commander, the risks were known, the dice thrown. In this instance, the numbers came up wrong for the OP, he and he alone decided to put in an inadequate FSD, no one else.