As an Iranian ex-patriate, there are few people who resent Islam and Khamenei more than me. Few people would be happier if they never had to read another word written by him or see his hateful scowl ever again.
But this comment is a terrible response to his "open letter". It betrays an ignorance of Khamenei's position and power, his aims, views, and so on. It even slightly disparages the average Iranian by disregarding the very few good things we have going for us, for example that contrary to much of the rest of the Middle East, terrorists actually don't operate comfortably in Iranian society: it's extremely secure, almost no one has guns, there are almost no shootings or bomb blasts, and Iranians typically don't sign up to blow themselves up in other countries.
It sounds like this comment was written by some rage-ridden middle school kid who imagines all of Middle East to uniformly resemble some torn up desert landscape with "Freedom"-hating terrorists shooting AK-47s in the air in a sandstorm. Is no one else going to come up with a better rebuttal to Khamenei's letter?
Khamenei knows full well the power of words, and this particular letter is very carefully crafted to get the attention of the thinking youth, and to make them question mainstream narratives. It sounds good on the surface, but the devil is in the details. He sneaks in phrases like 'their recruited terrorists', alluding to the Paris shooters, seeming to imply that the shooters were recruited by Western governments to plant a certain image of Islam in the media. This is the typical paranoid world Khamenei lives in: he actually believes those things. He thinks it's all a giant conspiracy against Islam and non-Europeans. If you notice he keeps referring to 'they', a certain nebulous group of bad guys that he never clearly defines. He does the same when he gives speeches in Persian, where he keeps referring to 'the Enemy', without ever specifying who exactly that is. He does exactly what he is accusing the West of doing: exploiting a fear of the "other".
Khamenei is not stupid, though he seems a little gullible (fooled for example, by the former president Ahmadinejad). I don't think he's even particularly religious anymore, though he deliberately utilizes religion as part of his mechanism of political power. He is someone who on some level genuinely wants to help the people his country, you can even tell he genuinely values things like scientific advancement given how much he tallks about it. But he is destroying Iran slowly by being a deeply paranoid, bitter, and twisted despot who is intolerant and fearful of dissent and reform. His political decisions are guided by certain paranoid principles that he hangs onto obstinately, for instance he thinks if he were to show any public weakness whatsoever, and retreat from his long-held positions a single step, "the Enemy" will fully overrun him and all would be lost. This mentality is a huge factor in the long-running stand-off between Iran and the West.
I didn't mean to write this much. I was just hoping to point towards a direction where the right context to understand this letter may be found. It's not for me to write a response to it: I'm not a Western youth. I was just hoping someone else would do a good job.