The link provided in the question has many good and convincing arguments as to why questions related to Creationism and Intelligent Design should be categorically viewed as off topic. They are asked to advance a position that is in no way related to scientific discourse. I also think that considering the size of the community and the activity on meta, that there were more than enough votes to adopt a no tolerance policy for Creationist and ID based questions.
What you have right now as the rule is that only the truly horrendous questions get booted. The reverse should be true. The rule should be to categorically reject, except in the exceptional case that the community feels that there is a greater worth to the answer being provided. It should be no different to the handling of subjective questions. There are the rare few that are tolerated, and only when they lead to truly outstanding answers, such as this question related to evolution (though an actual science question and not an ID couched question) should they be allowed to stand.
I would add to that that as SE is positioned as an Educational Site that we take a lead from Kitzmiller v. Dover Area School District, where the decision was that ID and Creationism had no place in a scientific educational setting and that even the forced acknowledgement of controversy was out of bounds as the controversy was only a way of advancing a religious ideology as a result of the fact that no scientific controversy actually existed.
To address Terdon's points
1) If someone is actually interested in clarifying misconceptions that they were indoctrinated in, there are ways of asking the questions that seek out that clarity without bringing those misconceptions into play in the question. I think sometimes we think that the Poor IDers are uneducated, so they do not even know how to construct a question without falling back on bankrupt ideology and rhetoric. The ability to ask an appropriate question (site appropriate question) has nothing to do with ones beliefs. If the poster cannot formulate an appropriate question that asks for facts without bring ID into the question, then it should be closed, as policy.
2) As with 1, there are ways to ask a question and ways to not ask a question, and if they cannot come up with a question that leaves out ID or Creationism, then those are bad questions. Remember that it isn't only that a single question could have a good answer provided, it is that the questions are chaff and the more chaff that builds up on the site over the years, the more difficult it will become to find the insightful questions, as they will get buried under salacious questions that get caught up in ideological voting wars. Take this question. While it is closed, the question itself prompted 30 upvotes with an overall positive vote of 25. The top rated answer received 87 upvotes with a total score of 78, even though it is primarily opinion based and the references that were added after it was pointed out that there were none are, at best, week. So for arguments sake, if the question had been allowed to stand, it would have been one of the top rated Evolution questions on the site, and that becomes the face that we would be putting forward for the world to see.
The fact that there is a mechanism that allows for questions that are too broad to be removed doesn't mitigate the need to have a no tolerance policy for all but the truly exceptional questions. As such, there should be a specific mechanism to address ID/Creationist questions for removal.