I think it's the right thing to do. Like he said, a little girl was kidnapped from his fleet by the Cylons, and they need to go get her back. They've already lost so many people, and he's going to do what he needs to do to prevent further loss of life. Roslin outlawed abortion because every single life is important when there's only 39,000 of you left. Hera is just as important as anyone else.
And yeah, as character-driven as this show is, it's frustrating that they're still showing backstory for all these characters when there's only 2 hours of show left. Any sort of resolution for Starbuck is going to feel tacked on at this point. I don't see how they can successfully resolve that one.
As a side note, is there anything from the Last Supper pic that we haven't seen resolved yet?? We know now that Helo and Athena are reacting to Tyrol, because of Hera's kidnapping. The one thing I don't get is that they showed Natalie, the brunette Six, and said a new Six will establish leadership in the Cylons, but it was a Caprica (blonde) Six that did that, did they think the model of Six was irrelevant??