Yes, suck half a quart back out!!!!!! Over filling an R3 will blow oil out of the valve cover.
The bike holds 5.5 quarts and the tank will only hold so much, if you overfill it the oil has no place to go and will blow out of the engine. That is why it is so important to not check the level and add oil after the bike sits awhile. The oil could have leaked back into the case and not really be low at all. An accurate level can only be checked after its had a chance to run awhile and scavenge all the oil it can from the sump.