I would say they are getting one over on you, I find it hard to believe that the entire shifting mech needs to be replaced. Sounds like a lazy tech, that does not want to measure things and actually take the shifter mechanism apart to replace the parts that are faulty. Sure its easier for the tech to replace the whole mechanism, but it ends up costing the customer (you) and gives ducati a bad name.
When did your warranty expire? Usually they would goodwill that repair if your warranty just expired. Exactly what parts are they replacing? I find it hard to believe that the lever is bent unless the bike was laid down. Did they already split the side cover open to see inside? If not they are trying to get the best of you
The 7500 mile service is usually in the 1000 dollar range, but that is one of those things with ducati service.
Let me know what they are replacing, but my suggestion would be to take it to the dealer in Ocala, Sebastian is the owner and master tech there and he is the best!