I can't find it right now, but someone from Southwest indicated that F9 miles would eventually move to Rapid Rewards. IMHO, you can take that to the bank.
Rapid Rewards is due for an overhaul early in 2010, and the new program is expected to resemble Virgin America's Elevate and the relaunched JetBlue True Blue (which we call TrueBlue2 here).
If I were running Rapid Rewards, I would delay merging F9 miles until RR 2.0 begins. Why? Because RR 2.0 will be much less favorable than today's RR for some customers. Those people will be upset. Southwest doesn't need to add F9 customers to the ranks of those disappointed by the change to RR 2.0.
Edited to add this link to discussion of RR 2.0:
http://www.flyertalk.com/forum/south...on-thread.html