I know for a fact that a half quart too much oil can be added without any problems. However, if you actually had oil flow up out of the fill hole when you popped the cap off, you've got waaaay more than that in there.
Too much oil will not *hurt* the engine if you're not pushing the engine really hard. What will happen, though, is the engine will act just like a pump and start ramming all that extra oil up past the piston rings and up thru the crankcase breather system, and all the oil will end up flowing thru the intake system and into the combustion chambers. The engine will start billowing white smoke and if all the oil isn't cleaned out of all the little passages in the air intake system, small pieces can get gummed up and the engine won't run well until it's thoroughly cleaned.
If you have a ton of extra oil and you're flogging the engine (riding really hard, full throttle, hard acceleration, etc), then you can do physical damage to the parts because the crankshaft and connecting rods smack against the surface of the oil as they rotate.
As said above, open the drain plug and let some of that extra oil out. An R6 uses less than 3 quarts of oil even with an oil/filter change. Hold the plug against the hole with your fingers, and remove the plug in 1-second increments. After each second, thread the plug in a little ways so it stays, and check the oil. Repeat this until the oil level is back to normal, then tighten the oil plug.
*edit* Hey, I have a question for you...when you filled the engine with oil, was the bike leaning over on its kick stand? That would explain how you managed to get so much oil into it that it flowed out of the hole when it was straightened up.