I don't have a problem with Emma having guilt over how her actions effect Regina. It's complicated and messy emotionally. I see it as Emma following her instincts to save a life, but then realizing that her actions hurt someone who has been making good effort in her life to turn away from her darkness.
The guilt, if they play it as that, wouldn't be stupid. It rings true for her character to me. But hey, that is just my take.