While I appreciate your argument I think its harder than you may believe. Attempting to explain away pseudoscience is difficult, because you must give air time to the pushers of pseudoscience. And as you note, many (most?) scientists are horrible at explaining their ideas, pseudoscientists are often quite good. And one of the reasons why they're quite good is they latch on to common fallacies that non-scientists have.
Try it. Take a patently false position, but base it on something that might resonate with people. Here's an example... global warming. I bet you could convince most people that a possible explanation of global warming has to do with changes in our distance to the sun based on the gravitational pull of Jupiter. I know... I've done it.
Another example is autism and MMR vaccination. The arguments for it sound pretty good, especially to those that have children with autism. The problem with the argument against it is that it is simply that, an argument against the vaccination theory. The next question you get is, "So if it's not that then what is it...". Of course the anwer is that we don't fully know yet. To many people this hole effects the credibility of your original refutation.
I just say this to say that the road is tricky, and giving air time to people who push pseudoscience I think can (and usually will) do more harm than good, given the state of the world today.