The vertical shooter in the game is pretty easy and a nice interlude, i wouldn't sweat about it. You might consider to give, instead, a minor consequence to losing it. Like, next scene, the shuttle background looks heavely damages when the droid gets in, MC brother complains some technoblabla like that the life support is about to fail and when MC is later rescued it is mentioned that the main ship's crew barely menaged to recover the derelict shuttle and save him.
I believe this shouldn't give you too much extra work and it would give a sense of agency to the player.
The idea is not bad
in the next issue this mechanic should be added let me know if that's what you meant next.