I've found that I've earned far more Starfleet Merits than I could ever possibly use promoting my officers. I think if you just wait it out for a bit, you'll find yourself drowning in them too.
Starting out Starfleet Merits will be in short supply. Especially if you rename characters. As you get higher level you have a plethora of Merits. But to answer you question, no. You can't earn Merits only w/o earning more Skill Points and BO Skill Points.
As you earn more grades, you'll be given new BO Candidates. You might find replacement of the misnamed BO among them. That is how you get the the Uncomon, Rare, and Ultra-Rare BOs. Oterhen then purchasing them on the Exchange.
It might be cheaper to hire a new BO and retrain it, depending on how much you've spent on the original. You can recreate the original design by saving it at the tailor.
Captain: Lt. Avenger! I'm renaming you to Lt. Expendable.
Lt. Expendable: But I like the old name better.
Captain: Well, you see, I just scored a very rare bridge officer. Here, try on this red shirt.
Comments
As you earn more grades, you'll be given new BO Candidates. You might find replacement of the misnamed BO among them. That is how you get the the Uncomon, Rare, and Ultra-Rare BOs. Oterhen then purchasing them on the Exchange.
Captain: Lt. Avenger! I'm renaming you to Lt. Expendable.
Lt. Expendable: But I like the old name better.
Captain: Well, you see, I just scored a very rare bridge officer. Here, try on this red shirt.