That's would be comparable to how movement in space actually works, only instead of low acceleration and high top speed, it would low acceleration INFINITE top speed. However, that would be kind of annoying to deal with.
one thing that could work is have the engine boost you get with lowered shields and no weapon fire scale based on the size of the ship. The larger the ship, the more boost they get. They still shouldn't be as fast as frigates for gameplay reasons, but it can be enough to make moving large distances a bit less painful. This would make a lot of sense, because capital ships require a lot more power for combat systems, but when those systems aren't in use, they can throw that power at the engines. (this could also allow fleet's to move faster)
btw, does the boost to speed also effect turn rate? if it does not, then it should.