(I have an extended version on Practical Ethics)
My general approach to tolerance is to tolerate those who tolerate me as well as those who tolerate others in my network of tolerance.
But that is a general heuristic: there are plenty of people whose views that I might tolerate in general, yet hold particular views that I think should be criticized roundly. This is of course not intolerance, which generally calls for discrimination (institutional or informal) against people with certain views. However, I do think I am justified in being intolerant against intolerant people - both for reasons of my own and my society's self-preservation, as well as to maximize liberty.
Should we then be intolerant against people peddling bad science? I think at the very least we should call them on it, and possibly even go a bit further. The reason, as Beddington points out, is that "We should not tolerate what is potentially something that can seriously undermine our ability to address important problems." Insofar science and clear thinking help us live better lives, lack of intellectual integrity that undermine these are actually bad for our lives. If problems cannot be solved or recognized because of noise, deception or bullshit then the moral thing to do is to try to reduce these sources impairment.
It is less clear how far morally one can go in pursuing intellectual integrity. Censoring pseudoscience is problematic, since freedom of thought and expression are also quite essential for the epistemic function of our society (not to mention that plenty of pseudoscience shades over into fringe science that could be true, but with a very low probability). Many false claims are made out of sheer ignorance or laziness. However, deliberate distortion and deception seems to be a promising target. Even there finding appropriate standards might be tough.
But at least we can make it a social rule that just as we frown at racist, sexist or homophobic statements we frown at pseudoscience or deceptive evidence.