Why does the gc content deviate from 50% in prokaryotes
Interesting question. I think that bacterial GC content diversity boils down to a mix of mutational biases, such as using different polymerase and replication/repair gene isoforms, and environmental pressures, such as temperature and salinity, that have placed different selection pressures on the various microbes. 

I would read over the linked papers for more detailed info, but at least in broad strokes, I think that the two mechanisms listed above account for most of the observed variance.

NB: This isn't my main field, so you might get a more detailed answer if an actual microbiologist weighs in. :-)