This sounds like Quickstone, by Marc Laidlaw, in the March 2009 issue of The Magazine of Fantasy and Science Fiction. (cover at the bottom) You can buy a copy here.
Gorlen has his arm switched with a gargoyle named Spar. At the end, the goblins are destroyed by their deity, except for Spar and Gorlen.
The description in the magazine:
When the bard Gorlen returned to F&SF in our August 2008 issue, we promised you'd be seeing more of him soon. Promise delivered (and there's more yet to come!). If you haven't read any of the previous stories in this series, dive right in - you should have no trouble following this story of the bard with the gargoyle hand.
A scene with both the switched limbs:
"I owe then nothing," Gorlen said, "Except this."
He held up his right hand.
Spar sat for a moment regarding the black digits with something like adoration and pity. He reached out first with the white flesh hand, then drew that back and put out his stony left hand to touch its prodigal partner.
At the end, when the other gargoyles are destroyed:
The blazing blood of the God engulfed the platform like a sea wave smashing on a rocky shore, washing away the other goyles.