If you want to just mute a note in the Graphic Editor instead of deleting it double click on the note which brings up the note editor and then enter 1 in the Velocity On box which should mute it. It's a little easier than pinching off the stem with the Velocity tool.
Some instruments such as many of the Garritan instruments use modulation as velocity and velocity as attack. In this case you can probably just pull it up or down to a note out of the instruments range and pull it back to use it.