From both a flavour and gameplay standpoint I think Safety Overrides don't make sense on cruisers. Frigates and destroyers, fine; there's few enough moving parts that overlooking regulations is somewhat managable; but on a Cruiser there'd be so many little things going wrong that you'd have more crew trying to stop the ship from flying apart than actually manning the ship.
From a gameplay standpoint, there's a vague dichotomy of speedy/short ranged ships vs slow/long ranged ships in StarSector and SO basically pushes ships towards the speedy/short ranged side. Frigates are naturally towards that end already while cruisers tend towards the other end, so in many cases SO on a frigate or destroyer is playing to its strengths (and thus less of a paradigm shift), whereas SO on a cruiser tends to be turn about making the ship something it isn't (i.e. a big paradigm shift and used as ammo for some people to say stuff like "Eagle is fine because of SO").
So my thought is that SO should just be banned on cruisers. Yes that includes the Pather Colossus because let's be honest, it's not doing that much good on that ship anyway (and could easily be replaced by something like Unstable Injectors, plus the new Pather Venture won't have SO either).
Does SO need further nerfs if it can't be used on cruisers? I think probably not. Most it might need is a bit of a nerf on destroyers only, maybe a bigger PPT debuff on destroyers compared to frigates to represent how much harder it is to keep a larger ship from flying apart when you disable all the limits.