Some ways would clearly do that, such as forcing the upper boundary layer to detach. But that sounds like a pretty extreme approach (although possibly very easy and quick to implement). On the other hand, for instance increasing the angle of attack would typically increase both lift and drag, although much more lift. Lowering the flow speed on the upper surface might actually lower drag. Anyway, surely the lift due to the engine shape is pretty small, only an issue because of its location so even if the drag would increase somewhat it would likely not be very significant.