My interpretation was that he wobbled as he fired (he was quite drunk, remember) and managed to score only a glancing hit, the bullet grazing his skull. I think this is common enough, and this is why the prefered method for such a deed is to place the barrel in the mouth.
Pistols of that era CAN kill. After all, the pistol used was taken from a set of dueling pistols. They can also have a bit of a kick, though. They're not too accurate when firing at another person standing several feet away, but placing one to one's forehead & pulling the trigger will normally get the job done. I'm guessing he was too drunk & unsteady to hold the weapon properly & when it went off the kick was enough to move the muzzle at the last possible second.
Karl van Beethoven did try to shoot himself in the head in real life. From what I recall (from biographical texts), the gun supposedly misfired. That could mean that the bullet didn't come out with full force, or it could even mean that the bullet never came out at all, and it was the explosion/shrapnel that gave him the head wound. Details are sketchy, but I think the movie handled it pretty well.
Maybe he was just scorched as he lifted the gun? Anyway must be quiet some punch. Imagine the *peeeeeeeeeeeeeeeeep-sound* in your head after such knock... *peeeeeeeeeeeeeeeeeeeeeeeeeeeeeefffffffffffffffffffffffwwwwwwwwwwbbbbbbbbbbbbbbb.....................zzzzzzzzzzzzzzzzzzzzzzzzzzzz* Ok, that's how Ludwig Van must feel like all his later life ;)