Sir, the pluses that I see are as follows.
1. The Naval Yard
2. One more port for blockade runners to use.
3. One more port for Union blockaders to cover thereby spreading them thinner (at first)
Minuses
1. Manning required that could be used elsewhere
2. Perhaps the loss of the desperately needed rails that were ripped up from the Alabama & Florida (of Florida) RR - please see
@DaveBrt 's
http://www.csa-railroads.com/
Questions;
1. Does the Confederacy have the resources to benefit from the utility of the naval yard vs. the cost of defending it?
2. Does Pensacola provide anything Mobile doesn't?
Cheers,
USS ALASKA