So to answer the OP, I think your snake will be fine just try other methods of thawing - it's kind of a trial-and-error game. Everyone does it differently, and many methods will work.
There will only be an issue if your snake regurges the meal, but it doesn't sound like that will happen to me.
(I personally don't even bother with water while thawing, just set it on the counter in a baggy. I'm lucky enough to have a partner who doesn't care, and no other pets to bother with a dead mouse/rat).