I don't think the flare gun specifically is that good an idea for a piloting tool, because it works really well as a gun and because of plenty of reasons OTHER than the potential for abuse.
That abuse problem is a big reason, but it's not the only one. And I'm sure there are other possibilities for piloting tools that DON'T require the helm to be useful, some of which may or may not be open to abuse.
Maybe they could change it so a non-pilot can take tar and use it on an engine to trigger a small tar cloud but cause minor damage to the engine. It wouldn't be an ongoing effect like the pilot using it, and it wouldn't continue damaging the engine over time. It would have to trigger a cooldown on the engine as well, delaying repairs slightly, but it could be a helpful tool for an engineer. You could retain the helm use as well, of course. Maybe they could do similar with non-pilots being able to trigger impact bumpers on the hull armour with a combined cooldown/effect duration and an instant "stop" effect when it's triggered rather than the speed reduction over the duration of the effect. Obviously, these effects couldn't be triggered on broken parts.
EDIT: Also, I acidentally "inspired" a Captain to run around his ship loading Lochnagar ammo into all the Flamethrowers... Oops (helped out my team though, he was an enemy). At least we found out how well that doesn't work, I guess...