Kirks Enterprise was under construction in 2255. It may very well have been named already then, with the then-existing "Enterprise" being scheduled for decommissioning upon the completion of the new Enterprise. 3 years later, we see the completed new Enterprise, that doesn't mean it was completed on that specific day. Most ships go through a "shakedown cruise" of about a year or so, and not necessarily with the same crew that eventually is assigned to the commissioned ship.
Fan-fiction for the Enterprise-E, suggests that Captain Bateson (Kelsey Grammer, in the Cause and Effect episode) was in command of the Enterprise during it's shakedown, prior to Picard and crew being assigned to it in First Contact.
In any case, anything that is written in a comic should be taken with a heavy dose of salt. But I see no contradiction in there existing a decommissioned Enterprise in 2257, when the new Enterprise was eventually commissioned by 2258.