Probably an unpopular opinion, but capital ships aren't meant to be fast and agile. They're meant to be able to both deal and take insane amounts of damage. I mean, we're talking about ships that weigh tens of thousands of tons and are hundreds of meters or even kilometers long (1 block unit = 10 meters according to koonschi), they shouldn't be able to stop and turn on a dime.
IMO removing the thruster spamming exploit would be a very good thing because it would force you to rethink your ship choice. You could no longer just build a single massive battleship that does all the things. You would actually need an entire fleet and the composition of the fleet would determine its strengths and weaknesses. This would also bring a ton of depth to multiplayer PvP because it wouldn't be "the guy with the biggest ship wins" anymore.
Tl;dr: I, for one, want capital ships to be slow, lumbering giants, ideal for destroying stations or other capital ships, but useless against targets that are significantly smaller and/or faster.