There is an even easier solution to the "use of fuel" idea but from another angle....
Make the cloaking "device" actually a level 10 gun, or an energy using device from panel one of the onboard equip screens. Maybe even a fulltime burning shield replacement.
Make the "gun" or "shield" an "auto-fire" once activated and you will see your energy bar start falling like a rock. Actually, you could even make it force-out the use of guns while in cloak.
The timing of the cloak has to be energy based anyway and I would think you can pre-fix the burn time to make the use of it worth the cost and loss of a gun and/or shield.
Once the energy runs out, guess what? No cloak, and no guns either until the bar restores to functional levels.
The advantage here is:
(1) you have to lose a gun or some other "important" object;
(2) it would be used less in sneak combat since you are a gun short as well as no power to use guns or in a limited way depending on power restrictions placed on guns.
(3) Primary use would be more for traders and others getting past bad rep NPC systems safely.
It's just an idea, not sure if it is even feasible.
I would say if the addition of a cloak costs more headaches for OP and disrupts the dynamics of the game, then I vote for no cloak.