Having given the subject some thought, the way I would treat enlisted personel would be to classify them as having the Starfleet Officer profession (with its attendant list of professional skills), but deny them the ability to take the Starship Duty professional ability (they can have it when they decide to go to officer canditate school, or recieve a field promotion into the Officer ranks, etc.).
I would also make a few slight changes in the published rules for picking skills. As the enlisted character is no doubt assigned to a particular department, I would allow the five picks allowed for Engineering, Science, and System Operations skills to also be spent on the skills listed under the Elite Profession corresponding to the department (basically so you could build an enlisted security guard with Observe and Investigate or an orderly with some First Aid and Medicine if you felt so inclined; the other professions can be pretty well covered with just Engineering, Science, and System Operations). Only the listed Starfleet Officer skills and those additional skills acquired with these five picks at character generation would be considered professional skills for purposes of advancement (if you want to cross-train, pick up Rounded). I would encourage favored Abilities and Reactions to be chosen from the appropriate Elite Profession.
This sound like a reasonable set of house rules to anyone else?
-Chris
"Was entstanden ist, das muss vergehen. Was vergangen, auferstehn." -Klopstock & Mahler
"Only liberals really think. Only liberals are intellectual. Only liberals understand the needs of their fellows." How much viciousness lay concealed in that word! Odrade thought. How much secret ego demanding to feel superior. - Heretics of Dune