Thats very high on the price and is not the standard... depending on how much of the car you are going to get covered. My rate fro the full hood, full fenders, bumper, lights, mirrors and rocker panels is less than $1500... so you might want to look for another installer. Second there are no issues at all with removing film from factory paint. I have replaced film on dozens of cars and not one single issue with factory paint. The only time to worry about that is if the film was installed on fresh paint that hadnt fully cured. Then its a potential issue... or if the quality of the respray was poor. But anytime you respray a car you kill the resale value as people will assume it was damaged in an accident... I have seen this happen numerous times. And finally there are numerous films out there that have come out that are very resitant to yellowing. Suntek, Xpel Ultimate, and Avery Nano Fusion are the best new films out there. If there is yellowing then have it replaced under warranty. Its that simple. As a side note most of the yellowing issues caused before were due to using products on the films that contained petroleum distillates... which have a chemical reaction with the urethane and causes it to discolor. If you use the correct product on the material (Zaino is a great product) then you will not have any yellowing issues at all.
By the way, reach under your rocker panels and tell me that maybe you should haev gotten film installed. They get destroyed under there... my 2004 had film installed when it was brand new and 20,000 miles later not a single pit on the rocker panel... or anywhere else for that matter.