Not sure why me wading in is going to change anything, but looking at that busted carbon site, there is an entry on June 30th with a busted chainstay.
The description reads "Just "Popped" when I stood up to do a fast sprint around a slow rider on the local W&OD bike trail."
So to me, that could well be similar to the scenario we are presented to here when you consider that the guy on the other website stood up to do a fast sprint, we can only ever assume but my guess from my own sprinting experience is that he was in a fairly high gear which would have put a lot of load on the chain, not too dissimilar to having a chain being too short and with an awful combination of being in a massively high gear as well. This with the honking of the rider literally standing on the pedals putting through their whole body weight and more through the crank arms in a non-linear fashion (we all sway from left to right ever so slightly when dancing on the pedals don't we?) would have caused a lateral force (I think) on the chainstay which could possibly snap it.
Now if say the OP's friend was descending in this large gear and then proceeded to climb in the big gear and then actually stand up (again only presuming as none of us have facts), then the same thing could have happened. Now, if the chain had not been shortened, then yes the frame would not be fit for purpose as whilst being in a big/big combination is not ideal, it is by no means forbidden therefore i'd be expecting a replacement. However for all intents and purposes the bike has been tampered with and thus Specialized IMO are well within their rights to refuse a refund based on this. Even if there is no conclusive evidence that the shortened chain has actually snapped the chainstay.
My credentials btw is an honours degree in History at Coventry Uni and a Physics GCSE. Make of that what you will.
Thanks.
Jon.