I got to say that is a load of crap from them. You cant fun 35" tires on a D30 front? Folks with older Jeeps have been running 35's forever on the 30, and get on any major forum and look at the number of members with 35's on the JK and very few issues reported. I ran 35's on my front 30 for 26k miles and I wheeled it a lot in that time (and it came new from the dealer with 2.5" lift and 35's).
Anyways, good to see so far they are trying to fix it warranty wise and not fighting with you. Whats the dealer name?