I've been thinking about this.
IIRC, the only thing Mellissandre said to Stannis regarding her latest vision was that she saw Bolton's flag burning, etc. If that was truly the extent of her vision, things may not be as they seem.
The aftermath of the battle showed tons of bodies. While obviously the assumption is the majority were Stannis' troops, we really don't know how bad the Bolton forces got fucked up. It's quite possible they are very depleted, and now are ripe to be taken out by some other attack.
Could the answer be as simple as Mellissandre completely misinterpreting the vision to mean that specific battle would go Stannis' way? That's the thing with visions, you don't always get the context. It's quite possible the vision was true in that Bolton will ultimately lose, but it simply wasn't from that battle. Moreover, that battle may have in fact been necessary to set it up?
The other interesting point is that they never showed Stannis being killed by Brienne. Given the above I have been wondering if Brienne will somehow take out Roose and Ramsey now that they are depleted. But now that I think about it, Brienne may actually have spared Stannis in order to help take out Roose and Ramsey for all we know?
So while Mellissandre's faith could in fact be shaken as things stand, it's quite possible that will change with the realization the vision was still true. She was simply the one that failed to understand it.
Hahaha What she was probably seeing was the aftermath of Littlefingers take over of Winter fall.