Because she wasn't in the command division. People don't jump between divisions every time they take on a roll on a ship. When Worf delivered Molly, I bet he wasn't thinking, "I really should be wearing blue..."
Though I wonder if Farrell just didn't want to wear red.
http://en.memory-alpha.org/wiki/Captain#Starfleet_captainsHowever, the rank is apparently obtainable in both the sciences and operations division, as the rank was held by Captain Krasnovsky in 2267, although he may have held command qualification while also being a science officer, and Vice Admiral Toddman presumably held the rank sometime before 2371. (TOS: "Court Martial"; DS9: "The Die is Cast")
Krasnovsky is the only character in Star Trek to be seen wearing a sciences uniform while holding the rank of captain. Jadzia Dax and Spock have held the title of captain in a sciences uniform, but not the actual rank. Leonard McCoy also presumably once held the rank, since he was an admiral in 2364, but wasn't seen in an uniform. In the real United States Navy, medical captains are very common as senior doctors in charge of Navy hospitals. The Surgeon-General of the U.S. Navy is a Vice Admiral.
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