I’m afraid I don’t think preferring a different charity necessarily indicates “ignorance”.
Your colleague’s remarks were perhaps rather tactless, but nobody is obliged to support any charity whatsoever, and, if they do, it’s entirely their choice which one(s). The problem is that there are so many worthy causes - nobody can support all of them, so difficult choices have to be made. You apparently think the other charity was somehow less worthy - not everyone might agree.
Do you think perhaps there might be a marketing issue, because of the particular sponsored activity you have chosen?
If I try to put myself back in the position of knowing little or nothing about MS (not easy, as I’ve been diagnosed with it five years now), I have to say an affected person “doing a run” might lead me to believe it wasn’t such a serious problem, and doesn’t devastate lives.
Please respect that charitable giving is just that - a gift. As such, no cause is automatically “entitled” to it - and certainly not more than any other.
I’m afraid, at work, I used to avoid these sponsorships, because of just this kind of problem. If you give to one, you end up having to give to all, otherwise it breeds exactly this kind of resentment: “Why was her charity better than mine?”
Please respect his right to say no. He probably would have been better just saying a polite: “No thank you”, rather than trying to justify it by saying the other charity was more important, but he’s entitled to his views.
Good luck with the run, and I’m sure that for everyone who says no, there’ll be somebody else who says yes.