Let me tell you a story. When I worked as a tech. We had a 2 week old car came in with brake problems (or lack of). After diagnosing,I came to the conclusion that the brake booster was the problem. While dis assembly I quickly realized that the "professional" installed alarm was the culprit. During instalation, they had drilled through the firewall, guess what, they had drilled the brake booster. The owner went through the roof when he was given the bill. Swore to take us to court, even filed a complaint with BAR. But it was the installers fault.
Why the story? Goes to show professional installer makes mistakes too. Sometimes once the damage is done, even if you remove the culprit its too late. I say at this point pay to get it fixed no matter what it cost, just make sure you have everything documented. It will come down to a point you can either go after your warranty if they cant prove anything, or installer if it was proven he damaged the car due to his work. Worse case call your insurance company see if they can cover the damages done.