Quite frankly, I can't remember the number of times I've blown the fuse on my M249, which probably saved me alot of motor burnouts.
But... I was running the frigging thing on a remote motorcycle battery, probably didn't help.
If I remember correctly, fuses in TM-style AEGs are rated for 30 amps, so before you reach a current anywhere close to that, the motor probably already overheated. Plus removing the battery 'compartment' frees alot of room in the handguard in the case of a M4 (another compromise would be to completly remove the fuse "plate" or "compartment" and wrap your fuse and both wire clamps in heatshrink tubing. It's going to ba a pain in the butt to change the fuse, but since it doesn't usually happen too frequently, it might just work as good for you, if the lack of room is your concern.