Reduce the gravity? But the gravity is my nice, nice little darling, are you suggesting I should kill my little darling?
Hrm... I guess you right. That and lower thrust force maybe. And maybe I should introduce a maximum speed to slow things down, even if its not very physically correct.
Don't kill your little darling, just slap her around a little
The gravity is a really cool gameplay element, but now as soon as a planet or something is in view, it's already too late.
I think the biggest problem of the game is currently the sense of not being in control, which is just a matter of tuning the physics of the game and balancing gameplay.
You can always increase gravity in later levels. You could also add some visual clues of the gravity, like particles going towards the gravity source, so that you will be notified of its presence earlier (and it'll probably also look nice).
Just an idea, it might be cool to add some gameplay elements from Namco's classic Bosconian: blowing up space stations, spy ships that might alert the enemy of you presence, alert states. (If you don't know the game, try it out in MAME, it might give you some ideas).