There are recipes out there that call for a mixer, but they must be executed carefully.
I used one myself for a ganache-like frosting that needs really a lot of stirring, almost impossible by hand. I tried by hand first, because I didn't trust the blender bit in the recipe, but used it in the end. (Turned out beautifully - and that was for my own wedding cake, so my expectations were super-high.)
Crucial point is, not to get any air bubbles into the ganache; once they are in, it's usually too late. I'd try Jefromi's advice and gently heat over a water bath, just to keep it liquid enough that the air rises to the surface naturally - stir occasionally and then perhaps skim the bubbly top layer. You will loose some of the ganache (don't throw it out, it'll still taste fine!), but perhaps the rest will be enough for whatever you need it for.
For your next try, if you can't stir by hand:
The trick to use a mixer - or rather: an immersion blender - is to keep the speed low (if possible with your blender) and the head right at the bottom and somewhat to the side of a high container. Do not use a shallow bowl. Make sure the "vortex" that forms while blending does not reach the head of the blender. Rather stop occasionally. Do not allow that "slurping" sound that happens when the blender sucks in air.