I think that the presence of that agenda does justify a deep skepticism, particularly since that agenda gives them a stake in a very sensitive culture war issue; namely what sort of presence religion is allowed to have in public schools. I have yet to come accross credible evidence of a similar agenda from the scientific community regarding evolution. The rejection of ID by that community seems to be based primarily on the notion that relying on the supernatural, something ID seems to explicitely do, is simply outside the realm of the discipline. I find this perfectly rational since it seems to work against science's goal of improving human life on Earth. By filling the supernatural in for what is not not currently understood, ID creates an incentive to explain difficult things away as God/the designer rather than delve deeper for more tangible explanations.
As for the scientists I have no idea what they believe or what their individual motivations are. I'm not a conspiracy person so I'm really not going to speculate on it though the pro-ID experts did not sound good in the Dover trial. One of the proponents of ID, Michael Behe even stated on cross examination that his definition of a scientific theory was so loose that astrology would qualify.
The transcript is here:
http://www.talkorigins.org/faqs/dove...r_v_dover.html (I'm not claiming to have read the entire transcript though I did read the opinion of the court)
Many hospitals and Universities are indeed religiously affiliated or were founded by religious groups but not all religions take issue with evolution or scientific principles in general. I, for example, come from a Catholic background and they do not have an issue with this. They teach regular old evolution in science classes in Catholic schools. Obviously there are plenty of problems with the Catholic Church (not going to delve into that either) but this isn't one of them. As far as I know most religiously affiliated hospitals aren't giving treatments that most medical professionals find to be profoundly flawed.