Dear God, just summarise your point. All I got from this horrible detour is that peer-reviewed doesn't equate to being good scientific research.

Too many points to summarise in one go, I'm afraid! But I'll try:
1. To say that a group that is against modern scientific consensus is "against science" is wrong. Those who argue against the consensus do so by arguing that it is they who are doing science right, and the consensus group doing science wrong.
2. ID proponents argue they are doing science correctly. They don't "reject science". They believe that the scientific consensus is wrong. But it doesn't mean they think therefore computers and planes don't work (paraphrasing someone's comment much earlier in the thread).
3. ID proponents are following the scientific method by (1) making an observation (flagellum), (2) proposing a hypothesis (IC), (3) submitting into peer reviewed publications. That's all good! That's science at work!
4. ID is a failed hypothesis, since the flagellum doesn't show IC. ID can be rejected as unproven. That's all good also! That's science at work!
This is very important to acknowledge. Science is under attack like never before. When one man can declare "I am the Science! To attack me you are attacking Science!" you know that science is in trouble. When science is devolved into "science is just those things that I agree with", then you get the same result if you devolve free speech into "you are free to say anything I agree with."
There seems to be an ideological line whereby even admitting that ID has had peer reviewed articles presented somehow means that science has failed. It hasn't. Quite the opposite.
It's a small hill, but one that I'm willing to die on. Hope that answers your question!