I think the issue with warranty is that the chain must've been hitting since the bike was built. Nothing has changed or failed, except you failing to notice the issue ! I'd have thought hub flange spacing is as much of an issue as freewheel spacers too- I know flange spacing and so chainline is certainly not constant between different hubs so would also affect things.
As has been suggested, flip your 12T cog round (might need a couple of shims to space it out a little depending on the hub, chain and sprocket) and use a freewheel spacer and the frame will probably last without any problem. Well, it'll eventually break somewhere but I doubt it will be where the chain's been rubbing.
Edit: *cough*