I had the same problem with my 2004 Beneteau 323. I actually did my own keel after attempting to get Beneteau to stand behind the repair. They declined stating that the issue was with the keel supplier who apparently is no longer in business.
The rework is no easy job, and unless you had the time and the tools as well as a yard that will let you do your own work, it's well worth the price you were quoted in my opinion. It is imperative that all of the old coating is removed and that there is no rust at all on the iron surface prior to re-coating. Hey, I had a cooperative yard, I'm retired, and am apparently a glutton for punishment, so I did it.
I used Interprotect 2000 and there is a time window involved for proper adhesion of successive coats as well as a time window for the first coat of bottom paint to properly bond.