Is $2,600 to repair a leaking small bump out roof a fair price?

A while back I posted here about my small low slope bump out roof that is leaking rain water into the wall cavity downstairs. Originally this cap was all one piece, but someone tiled over it, and I suspect that is trapping water. I am mostly shopping to see what contractors suggest, aside from price. Stucco would look better since that's my house siding, but I am not afraid it has greater risk to leak. If it's redone as a proper roof, it shouldn't leak, and they have a 10 yr warranty, but I am afraid it will look ugly, especially if there are seams. I can keep shopping around, but mostly curious what the proper job should be.