I had a motherboard fail on a 2011 MacBook Pro running Windows 7 - I just wiped the drive on another Mac and put it back in and have it to them. No questions asked.
I didn't know whether or not it would and for the 10 minutes it took, it was worth it to not have to stand in the Apple Store and explain why I was running Windows and not OS X.
If you had a hardware failure, did having a non-Apple-approved OS cause any problems when you tried to get it fixed?