It seems that CMI took a page from the producers of "Expelled" and set up a separate production company, and failed to disclose the nature of their production to the historians in question. That suggests to me unethical deception--lying by omission--though I'd like to know what exactly the historians were told and what releases they signed before they participated.
Updates to come if I find out.
UPDATE (June 27, 2009): CMI describes its process for the documentary, including the document sent to interviewees, on its website. No mention is made of CMI or a creationist slant to the film. The director says that "if anything, CMI’s influence was one of moderation, ensuring that all sides were fairly represented," but if he is himself a creationist and set out to make the film from a creationist viewpoint, this isn't much of a defense. Note that at least one participant questioned who was providing the funding, and was told only "private investors." And one participant tried to return his fee in order to not appear in the film.
The proof will be in the pudding--it will be interesting to see what the film's narration says and how they fit the interviews into it. There's clearly no defense if it says things that are false or misleading.
Implicit in the CMI position is that creationism is a valid, reasonable, and evidence-supported viewpoint that deserves equal representation, but that's not the case.
One thing that's clear is that anyone being interviewed for a documentary in the age of Borat and Expelled should do some due diligence before signing a release.
UPDATE: John Lynch has responded further, as well, and I agree with everything he says. Their statement about atheists having "no compunction to be truthful at all" is false and offensive, and their analogy to an investigation of the Communist party is a bad analogy.
UPDATE: P.Z. Myers has weighed in. This may be the sort of online media coverage they're hoping for--the film is showing at so few places that the biggest place in Arizona to see it is a church in Miami, AZ (population < 2,000).
UPDATE (June 29, 2009): The CMI web page contains this statement under the movie poster image: "The Voyage that Shook the World, CMI’s documentary, has atheists ranting and raging. Rather than critique the film, they falsely accuse CMI of deception." This statement itself is dishonest--the accusations of deception are accurate, and the current complaints are not necessarily in lieu of critiquing the film, if it becomes feasible to view it.
UPDATE: John Lynch responds further to CMI, and notes that he has been incorrectly identified as an atheist (he's an agnostic).