They work backwards, with the Bible as their basis of scientific knowledge. Pure science should examine the evidence in its own light; not according to what some old religious text says. Just look at evolution. Secular science tells us that we evolved over hundreds of millions of years, continually adapting to our environment. Christian scientists are forced to add God into this equation by such silly terms as "macro" and "micro" evolution.
I don't think this is true. I know many Christian non-scientists like Ken Ham, Kent Hovind, and Ray Comfort use these terms, and make the distinction, but they're generally pretty ignorant of science, and certainly aren't real scientists, or scientific researchers. actually it seems to me the concepts of micro and macro evolution were developed by a lawyer.
There are a few genuine scientists who look into distant concepts of intelligent design, but for the most part these people look at it from a different angle, and see it as a precursor to evolution, not in opposition to it. However, those investigations weren't going well last time I looked into it. I also tend not to agree with their methods for the same reasons you outline above, but I won't say the concept itself is invalid because of it.
That being said, I don't need to trust Christian scientists. In fact, a rule of thumb is that I only trust that scientists are being accurate in presenting their data. I don't trust that the data of any scientist supports their hypothesis. Any scientist can be wrong. Any scientist can be biased. Any scientist can make an error in judgment or logic. It's up to their peers in the scientific community to oversee their work, and correct them when they've made a mistake. It doesn't matter if they're Christian, atheist, or any other religious background. If everyone does their job correctly, it should all work out in the end. That's what peer review is all about.
Intelligent design was thrown out of a US court as a scientific theory several years back.
To be fair, a US court does not have the authority to throw out a scientific theory, even a really bad one. What it threw out was religious doctrine, disguised as science, which was intended to be taught in public schools, which was seen as imposing religion on students.
Intelligent design is a long way from validated as a scientific theory, but it's not yet invalid either. It's very difficult to actually show ID because (a) it involves investigating the supernatural through natural means (b) in order to prove that ID occurred, one must set up a method which could potentially disprove that ID occurred. That's tough to do.
In other words: It is still possible that Intelligent Design could be true in one of it's suggested forms. It's hard to imagine right now, but it's possible. Of course, New Earth Creationism is pretty much right out.
Sorry, I've started teaching a methodology class. It's good practice for me to try to explain these concepts.