I suppose it's been a while since I have had to say this, so here goes:
Your dealer cannot change the terms of your warranty. Your warranty is through Chrysler, not your dealer. If a dealer or anyone else puts something on your Jeep that was not there when the Jeep left the factory floor, it can void your warranty if that aftermarket (even Mopar) part causes damage to an OEM part. Your dealer can offer to warranty the work or parts that they install, but that is a separate and new obligation created by your dealer...IT DOES NOT CHANGE THE TERMS OF YOUR CHRYSLER WARRANTY. If you have to take your Jeep to another dealer, they are under no obligation whatsoever to service or replace the aftermarket part installed by the first dealer.
So, any dealer telling you that they will do a hemi install (or a lift for that matter) and that it will be covered by your Chrysler warranty is absolutely, positively, full of shit.