Sitting at 8 or 9 stability is pretty tolerable for a big income boost.
For income alone, 8 is enough to take the occasional -3/-50% from pirates. But high stability is important for things aside from income, especially since colony size is capped for the player.
(Also in my last game, most habitables had Decivilized Subpopulation - what an unlucky seed! I needed colony improvements just to offset that condition!)
It would still be worth it if you could get more stability by other means, I want a system wide stability boust by military bases, as they project major forces system wide and offer enough capacity to help with difficulties on nearby planets.
Currently, for player colonies, we have a net stability change of -1 from last release. Commerce for -3, and +2 from the two colony improvements that add +1 to stability. NPC core worlds with Commerce get shafted and may be prone to decivilization if they take further penalties to stability, like pirate activity and raids.
With our colonies capped at size 6, and one of the fleet doctrine stats nerfed, stability is important for fleet defense (and ship production without pristine nanoforge).
My 2 cents on a few raised points:
Commerce was the best industry slot for making money by a factor of 2.5 or more, but it doesn't supply any goods for reducing maintenance and has that stability penalty. I'm not sure if 25% is too harsh or not, it depends on how the item and upgrades are changed as well.
Atropos is a sidegrade to the harpoon but a useful one: it does slightly less theoretical damage per magazine (2000 vs 2250) in a shorter time and more reliably, with better tracking, slightly faster speed, higher projectile hitpoints, and better penetration value. Its main downside is being shorter ranged so you can't stack backline ships' Atropos from 2000 units away together, which is a big factor, but for brawlers its a superior missile (if you want to use missiles and not reapers).
Atropos is lame for brawling in part because it cannot be used point-blank - they bounce. Would be fine if they hit hard, but they are barely better than a Harpoon. Also, I may not want to use Reapers (because too slow or easy to shoot down without boosts), but I may take Hammer rack instead. I can hit one out of two and still do better than Atropos. If Atropos had more range, I might consider the homing a plus, but its range is too short to help much.
However, I might use (single) Atropos on ships with awkward mounts unfriendly for dumb-fire missiles, like say... Falcon or Eagle with those mounts way off-center.