I agree with Don and JC, and I'll throw in my .02 worth. If you have a warranty issue with something completely unrelated to the towing of a trailer, the dealer would be foolish to call out a "trailer infraction" and not do the repairs under warranty, Like JC says, it's definitely time to switch dealers (but not without letting them know that's why their losing business to Indian and that you'll be posting the dealer name on every forum on the internet). Hey, if they can play dirty, so can I.
If the dealer balks at doing the repairs on a tranny or engine problem, that might be a different story. Again, I have to wonder how Indian will handle this situation. I had 40k miles on the bike I towed my Bushtec with, and never had a warranty issue with it that would have been attributable to towing a trailer.
To me, Harley is splitting hairs on this subject, and isn't smart enough to see it's bad business.
"And professing themselves to be wise in their own eyes, they became fools..."