It should have some difficulty controlling its vector, depending upon atmospheric conditions. Some ships more than others. Having specialized craft that are built with specific types of atmospheric flight in mind, combined with the super powerful thruster tech of ED, would be a nice detail and offer some distinct gameplay.
Ultimately having some planetary conditions be beyond some ships capabilities (depending upon what those conditions are, the ship model, and how it is configured) is something I very much want. I'd like it if some high gravity planets that are landable, aren't just automatically survivable despite your configuration with very careful flying. If your thrusters are too weak then a controlled landing should approach impossible, and the ability to take off should not be a given.