More than likely, just a CYA move to ensure that should someone blow themselves up using it in a semi-auto, Remington can say "well, we told you not to use it, and even tried to get you to send it back to us." Over at Rimfirecentral, a Remington representative was asked about the ammo, and he replied that it was safe in bolt guns and single shots, but for some reason, semi-autos are bad news. I have an H&R single shot, and was instructed that it was safe to use Remington ammo in it. He also said, BTW, that all .17HMR ammo on the market is made by one company, and then farmed out to the other companies to package and market, so the ammo recall notice against using it in semis could be read to include all .17 HMR ammo on the market.
I think it is pretty bad that they are giving you a $10 coupon for a $15 box of ammo, though. And $250 for the laminated stock 597 HMR? Those guns are selling for upwards of $400 now... come on Remington, you gotta try harder than that!