I agree you should pick your battles. The phenomenon where people who identify as a certain religion seem to have a very limited understanding of what the teachings of that religion are, is pretty much universal. Because people get born into religion. Very few choose their religion. And they identify as it still because of tradition, habit and a sense of belonging. In a way the author of the story you read is correct. All the Muslims she know are just like her and wouldn’t resort to terrorism. Debating her on that is like saying the reality she is living isn’t real. There’s no way that will go over well.
What you seem to want, is a theological debate. I know from experience there are people from all religions who will happily and politely engage you in those. Someone might even present themselves on this story.
I do have to say though, Medium on the worst days is so much better than any other social platform I have seen in my 22 years of online interaction. If I have to have a disagreement online, I would prefer to have it here on Medium.