3rd is significantly short of ships, most of its combat power has already been expended. It does not appear an attractive target.
On the other hand, if you kill 2nd's entire command structure by knocking out the destroyer complete with Admiral and staff, there is a very real danger that Calder (as he commands a ship equipped to do so and presumably has the staff as well) will be given the duties for both Mars' fleet and what's left of his own fleet.
Before you conduct a decapitation strike, always make sure that you will not inadvertently give command to a better person.
EDIT: I think in the end my answer would be neither. I would probably elect to damage both ships or destroy significant portions of their escorts, and escape cleanly. At this point it's unlikely the UEF will be able to repair a significantly damaged Solaris, and with the command structure of the Rim fleet being essentially dead weight and the unpredictable results of decapping Mars' fleet, neither presents a a valuable enough target to justify their individual destruction when I can instead sow chaos by attacking two of the three UEF command ships and further cripple UEF logistics with a backlog of repair and resupply needs.