I would just talk it over with your service advisor and see what they are willing to do. Just 4wheeling your jeep shouldn't be grounds for not covering breakage on your warranty. Hell you can even pull out the "Trail Rated" mularkey on them.
Now if you went to different CA's and the mounts still cracked then no, they probably won't warranty that, because they have a good case stating that the replacement performance part caused the failure. However for stock arms on a virtually stock jeep then no I think they could be willing to work with you on that.
And to answer one of your other questions yeah I think it's starting to be more and more of a common occurence for those mounts to fail when used in conjuctions with shorts arms. That's a major difference between the JK and the TJ. You should see the mounts on the JK underneath. They are way beefier than what we see on the TJ's.