Can you not understand that whether saying it would cause problems is completely irrelevant to whether or not the statement is true? (Not saying it is, but that your statement is no rebutal.) I don’t read Chessic Sense as trying to say that we should tell them that they are evil, just that we shouldn’t completely avoid thinking about morality because you’ve explained their actions. Just because something is understandable doesn’t make it not evil. As you admit, these local religious authorities are keeping people from using Western medicine less because they think it’s really evil, and more because it resonates heavily with the population. They are putting their own political motives above their people’s wellbeing, which is a type of evil.
Not that your entire claim that people wanted you to say “Islam is evil” is not a complete strawman. The one person who voiced doubt in what you said did so because you didn’t clarify that you agreed these people were wrong in their beliefs about Western medicine. It had nothing to do with morality and everything to do with the fact that you explained everything so completely that it sounded like you might agree with them. Combined with your reputation (deserved or not) of thinking that the ways of other cultures are superior to our own, it led to someone misinterpreting you.
All you needed to do as a response was to say something like the following: “I thought it was obvious that I think Western medicine, being evidence-based, is superior to the magical thinking of other practices, but these people aren’t in a position to know that.”