There's Kurust that turns the rust blue which should be fine, however I'd be careful not to go OTT with what you use to cover it (paints etc.) as they need to scan the area, and if they deem it's been repaired before then they will say that the warranty/guarantee is void, esp. if they are trying to find a way out.
If u live anywhere near manchester i got mine done through old trafford vw. No mither.