[Legbreaker]

Well the city just got nuked. What help are they going to get there with the tens of thousands of other wounded already clogging the medical facilities (if any are left) before they can even dock? There may even be crowds heading to the docks looking for a way out of the city, and willing to kill for a spot on the ship.
Being a military vessel, they've probably already heard the first reports of strikes in other areas as well, so it's not a huge mental leap to consider follow up strikes where they are as well, especially given the facilities in the area they're in.
Also, if they were stern on to the first blast the bridge is very likely to have been spared the worst of it (a few casualties who may have been exposed through the rear facing windows and hatches). The bridge crew would be amongst the most important people on the vessel in the initial stages and it will take some time for them to assess the damage to ship and crew. While that assessment and initial reaction was going on, it makes sense to put as much distance between ground zero and the ship - they're already in poor shape, don't need fallout adding to their woes.

Once they were a few dozen miles to sea they'd be in a better position to assess their situation. Are they able to cope with their own casualties? What are their orders in this eventuality? Does their mission preclude assisting survivors? How widespread is the attack?
A lot of questions to try and find answers for before either moving on, or heading back in.