I went back and looked it up and it looks like the Crossfit article mentions research by William Kraemer when stating that the majority of isolation exercises don't elicit much of a neuroendocrine response. (The other argument was that you're unlikely to have to use isolated muscles in real life situations.)
I tried to figure out which Kraemer study they were referring to and found one that showed that single joint isolation exercises with controlled slow movement and no explosive lifting resulted in no development of power capabilities essential for athletes.
Kraemer, W.J. A Series of Studies: The physiological basis for strength training in American football: Fact over philosophy. Journal of Strength and Conditioning Research, 11(3): 131-142, 1997.
This of course doesn't prove anything re: combining explosive lifting with isolation exercises.
Here's another study by the same dude that suggests squats, cleans, deadlifts, etc. other large muscle-mass exercises should be performed before small muscle-mass exercises.
Hormonal Responses and Adaptations to Resistance Exercise and Training, William J. Kraemer and Nicholas A. Ratamess Sports Med 2005; 35 (4): 339-361