I’m not sure whether this is an anti science thread or an anti bad-science thread. Examples of lack of critical thinking exists in all areas, not just science and I’m glad to see that schools are now teaching critical thinking skills.

It's an anti bad-science thread. I find it very difficult to think that you are against science if you write in this forum. But disagreeing is essential for any debate.

I can only speak from the specific.
We are primarily an educational site to answer general questions posed by listeners to the podcasts, and readers of the articles. Listeners who pose these questions are usually looking for the current understanding on the topic. We often found that these questions were interrupted by people with their own theory or hobby horse. For example, a question about the moon’s orbit would attract a post by someone saying the answer was wrong because the world is flat not round; or a question on gravity would have the claim that gravity is due to air pressure and buoyancy; or someone else tries to interject aether or wormholes as the answer to most questions (these are real examples). In each case the original question gets lost because the thread gets diverted. So, it is necessary to draw a line about what can be discussed in the main section, but where do you draw that line? Some fora draw a hard line and will not allow any new theory discussion; I can understand that because they want to have an in depth discussion on quite detailed topics in specific areas. We take a more liberal view and will allow discussion in the appropriate area, but in drawing the line we are saying that many famous scientists around today would find themselves in the new/speculative section - and most wouldn’t mind.

Yes, where to draw the line? That's all about it. Normally forum means you are willing to debate. For example, if I go in a politics forum it's because I am happy to debate with people who have different ideas from mine, I'm happy to discuss, even if I disagree with them, I am not wasting my time, I can teach and learn  something. Why should I be afraid of different views, as long as they are polite, non offensive, there is nothing to worry about.
Another example. Let's say that you are into films, you like to talk about it in a forum. You will never find 100% of people agreeing with you, if you don't like Batman vs Superman, probably 99% of users will agree with you, but if some of them loved that film, and they disagree with your opinion, that's absolutely fine. They are into horrible films or they have horrible taste? That's fine, maybe it's a good occasion for them to learn something new about cinema. Another example, there is a poster who is an actor or an unknown director, and he posts clips about himself, maybe it's not that good, actually maybe you really dislike his clips, but what's the problem? As long as he's polite we can watch his/her clip. If the same person insists to promote his clips in a very polite but obsessive manner, in that case it's way too evident that he's using the forum not to discuss, but just to advertise himself, and this can be difficult to moderate, but if it goes to far, you can obviously ban this person.
Regarding science, it should be treated in the same way as any other topics. I would never use a forum to impose my view, a forum should be something totally different from snobbish elitist attitude, there is already peer review for that. And for educational purposes there is already  wikipedia/university, isn't that enough? Or you can create two forum sections, one for educational purpose (a.k.a the world according to peer reviews mainstream science), and another section for the constructive debate and constructive critical thinking.
Do I think peer review can be a good thing? Yes. But is it infallible? No. So who is going to disagree with the peer reviews? Allow the web to disagree and debate politely about anything.
Another example, someone here posts a new theory about a particle shaped like a cauliflower, this theory unifies everything and bla bla bla. What's the problem? You disagree with him? As long as he/she's polite, non arrogant, non offensive, where is the problem? 99% of users will maybe disagree with him, and will laugh reading his theory, but where's the problem? You can disagree and have a laugh at the same time, why not? After all this cauliflower theory is not so different from a string theory, is not so different from a multiverse theory, so why are you feeling threatened by new theories? So, in the end where to draw the line? In this forum I don't see many trolls, and yet if someone attempts to disagree with Einstein, his thread is moved to new theories.