Two options:
1. Accept offer from garage and go halves on a new roof (£550 cost is very good value).
2. As the car is still under warranty and the garage has tried to repair it at no cost to you (meaning they accept that it is a fault and needs sorting), then they should replace it entirely at their cost. If they refuse, which I assume they will, then go through SCC to sort it.
Option 2 is clearly the winner, however it's clearly going to take a while to get it sorted that way. You may be better off in regards to time and effort, but not financially, to take option 1. If you do go for option 2, make sure you get everything in writing, and that your warranty with them definitely covers the roof being replaced.