Is this principle part of natural laws? If not, is it supernatural? Otherwise, does it modify Earth bound DNA? Is it part of our DNA? Is it a result of the evolutionary process? What is this self organizing intelligence?
If this intelligence or the principle itself is a naturally occurring phenomena, then there is no need to replace methodological naturalism. If the supernatural is not part of ID (as it is being described in the attempt to insert it into education) then why the desire of Behe, Dembski and especially Johnson to replace methodological naturalism (materialism)? If it is part of nature then methodological naturalism would be quite enough to discover and analyze this intelligent design. This push by DI sounds like they expect the designer to be suernatureal.
I think their point is that the relatively recent presupposition of naturalism is impeding the search for alternatives, because it eliminates out of hand anything not conforming to current ideas on what is "natural". In other words, they are not asking science to quit searching, they are asking science to drop constraints that were not part of the earliest advances of science.