The balance issue for the Riot Starship is probably the low knowledge cost for a Mk I. A knowledge cost of 3 or 4 thousand would be more appropriate.
I think what we're seeing is that "long-range disabling of engines" is a powerful ability to have at all, much like "extreme high speed and the ability to shoot through force fields" (raid starships) or "reclamation" (leech starships).
Useful comparisons:
1) How many mk I bombers you could destroy with a unit cap of mk II fighters. I would expect the riot starships to be able to disable more bombers than the fighters can destroy, since disabling is a lower hurdle and the fighters have other desirable qualities (i.e. not weak against turrets, higher speed, quick to replace, good damage bonuses against many bonus ship types).
2) How much damage you could do with a unit cap of Zenith Starships. I would expect the riot starships to be able to effectively paralyze all the mobile ships on a planet if the Zenith Starships, in the same situation, would be able to destroy them.
3) How many bombers you can disable by building a unit cap of Spider Turrets in a system. Note that the spider turret is basically the immobile turret version of a riot starship; low raw combat ability, but disables engines from a great distance.
