1) Get an incredibly competent backup like Jeff Garcia (who will be available, fyi).
2) Order Manning to stop with the backpedal away from the hit as he releases the ball.
3) Put in your backup if Manning is unwilling to take the hit or if he gets hurt.
Plain and simple, Manning is not giving the team 100% as long as he ducks the hit. It is part of the job as QB to take the hit. And it is definitely part of the job when hanging in there with the proper (FOOT) mechanics means better throws and more hits. Take the high road and break this guy's bad habits. If he gets hurt and we need to go to the backup, so be it. Incidentally, if you signed a guy like Garcia he should be your STARTER. Imagine HIM throwing to Burress, Shockey, Toomer, Moss and Jacobs. TFB Eli. Think about how well Garcia did WITHOUT guys like this. NFL means 'not for long,' and without a quality backup, the Giants are not going to push Manning.
One more thing in defense of Manning- I would be willing to bet that Manning's dropoff in performance in the second half of the season is tied to the Coughlin grind. Yet another reason to get onto the next coach so that Eli loses the free ride and (he and his teammates) also gets an easier one late in the season.