For those who are interested by a solution, I solved it using a simple macro (autohotkey).

Strangely, remaping WheelUp and WheelDown to another key doesn’t work on FL (it’s remaped, but Wheel still have effect on throttle -.- ).
Even WheelUp::return WheelDown::return didn’t work.

So, I made a pretty simple script that “press” the EK key 1/15 of second after the wheel is used. With this macro, engine is activated during a so very short moment that it almost don’t have effect on Ship’s path. 🙂

Here is the script :

WheelDown:: send {v} sleep, 1 send {v} return WheelUp:: send {v} sleep, 1 send {v} return ```V is the key to kill engine, and don't ask me why I made it press 2 time, 1 time didn't work. In flight, it looks like it press it 1 time. I know this is certainly solvable by changing an offset somewhere, but I don't have the knowledge to find it