That could be done with the “shield acts as wing” mechanic. Lower cap ship thrust even more, but the shield could be … or even optionally have to be a module that needs to be installed, extended so it generates more lift. This way the capitals have to move in order to avoid stalling if engines get nerved even more.
Additionally, there could be an “atmospheric thrusters” options in the loadout that is easier to use but requires extreme sacrifices to be fitted.