1.) (more radical approach)
Cruise Engine should be moved to Spatial Scanner and Extended Hull, because they are GS modules only and as such, they should only be available in Open Space!
Those who have it, they don’t need to buy it, but it is only available to be purchased in the Store for the small GS price, for those, who don’t yet own one.
(You would have to make it so, that you cannot enter PvP, PvE, SQ battle with any GS (Open Space) module, which requires tweaking of MM!)
2.) (more realistic approach, or combined with solution 3)
This one is funny! You’re carrying a bomb! Bombs are sensitive!
Cruise Engine module has another hidden penalty. If you collide, while you’re carrying a bomb, you take 100% more collision damage from any form of collision, than you normally would.
One other thing. Maybe the bomb should explode, when you explode. It makes sense, because bomb is a bomb, but that would change how Detonation works and you would have to wait for another bomb to spawn.
3.) (most likely the best option)
Reduce the effectiveness of the Cruise Engine module by an additional 50%, which means that the speed is reduced by 50%, but not the handling itself.
4.) (probably too harsh)
Cruise Engine module is completely inactive, while you are carrying the bomb.