I can't find the thread where we had the discussion on how the Crossfit workout Murph should be performed. However, I have been vindicated!
Since the question about breaking this up comes up all the time, I asked Coach about it back in November -- here was his reply:
Michael Murphy's description for this workout included the following, "1 mile run, then 100 pull-ups, 200 push-ups and 300 squats in any order as long as the #'s were met, followed by another 1 mile run"
So, my interpretation is that "Cindy" style would be OK.
Hope that's helpful.
(Seriously, I've tried it "Cindy" style, straight through and a mix of both. All are ass kickers.)