Notoriety is a decent idea for minimizing ganking/griefing etc. It doesn't seem to work well with missions though.
The main problem with notoriety as applied to missions is that it was intended to discourage
unnecessary kills - and to this end, mission targets are exempt from notoriety.
Take an assassination mission - you won't get notoriety for killing your target, even if you incur a bounty. This is as intended. You
will get notoriety for any ships you blow up along the way that
aren't mission targets, such as if you decide to clear out the target's escort ships, which is slightly eh but honestly was never as effective as just blowing away the target and getting out of dodge.
The problem is that since odyssey launched there are now situations where you'll find a mission requires you to blast a guy but they're
not flagged as mission targets.
The
really super duper massive giant problem is that settlement massacre missions don't flag the base personnel as mission targets, meaning you have to blast something in the region of 20 people and
all of them incur notoriety. Notably, simple "massacre" missions, along with assassinations,
do mark the targets, meaning no notoriety for killing them.
Likewise, sabotage missions or heists? Guy hanging around near the mission objective who just won't sod off for three minutes and let you do your thing? He's not a mission target, so killing him incurs notoriety.
The
easiest solution that I can think of would be to simply negate notoriety increases if the player has an illegal mission at the settlement. You'd still incur bounties and lose rep though, so at least there's a reason not to blast
everyone.