You can take a small pair of pliers and bend the prongs 1mm fairly safely without snapping the prongs off.
If you need to bend the prongs more you can torch them. Be sure to be in a low lighting room and have the ring on a concrete block. Allow the silver to turn slightly red for several seconds. Pick up the ring with your tongs or tweezers and drop them in water. Repeat this process as needed until the stone sets low enough into the prongs.
Kendra wanted a low setting engagement ring so I had to go as low as possible with it. It helped that the seat of the sapphire is extra wide and has a rather obtuse point. Guy talk now... she's wider than she is tall. Back to specifics talk. I shaved down the inside of the prongs and ground away between the prongs to allow as much light as possible underneath without weakening the foundation of the prongs.