Although I would never be willing to claim that the end justifies the means, I would suggest that looking at the end point of the intolerance might be prudent.
I have little patience with those who reject others simply because they are different, when the difference has little or no real significance. I am, therefore, intolerant of racism, for instance; to deny someone a job, even though the individual is well qualified for the job, and the best candidate that has applied for the job, simply because you don't like their ethnic grouping (no matter what the ethnic grouping) is irrational. I do not tolerate that sort of thing well and feel that such behavior merits intolerance. Other examples should spring to mind.
Intolerance should, however, be celebrated in some contexts. 1+1=2 in every system but binary. Sorry, folks, but I'm totally intolerant of saying that 1+1=3 for large values of 1 and small values of three. It just doesn't; somewhere in this answers file, I mathematically proved 1+1=2, as I recall it. (Or was it 2+2=4? Whatever!) Where the intolerance is focused on rigidly saying that which is, is and that which is not, is not--well, gosh, I want that sort of intolerance in the engineering team that designs and the construction team that builds the airplane I fly on!!! And that builds the skyscrapers I'm standing in, and that engineers the elevators I ride on, and... Enough said!
Again, that's a results based thing. If the intolerance demonstrated demonstrably generates harm, it probably deserves to experience intolerance. If it promotes the good (as, for instance, in saying that the right answer to a multiplication problem is the right answer and not tolerating wrong answers), intolerance deserves toleration.
Of couse the sticky bit is that ther is a lot of life where we're not able to demonstrate the results of the intolerance, or where opinions about its result differ, or where people differ about what is or is not true. I make no bones about the fact that there is grey out there in life, and the fact that my answer is very much black and white based. For those areas where life is grey, my personal preference is to continue to labor to shed light on the issue until I can resolve it into multiple smaller issues that are closer to black and white, or into a single black and white issue. Some issues may never get there (Taste in clothes is a quick example) but I can live with that...
A lifetime of watching the human race do its thing, and doing a little thinking on my own