Hey!
So, I listened to Matt's video. I see his point about wanting to crawl the JS files just in case something tricky is going on. Do understand that this is a risk you take. I don't see an issue blocking crawling of those files from a logical perspective, but if you or someone that takes over for you in the future does do something sneaky with JS and you are caught ... plus you have blacked access to the offending files ... it is going to take a lot more work to get back in good graces with them.
It's like a cop searching your car. You have every right to ban them from doing so, but if you have nothing to hide, why make trouble? Matt is right, banning crawling of these files is not going to save you much but if you think it's an issue, feel free. Just know that they might take it as a possible flag in the future.
Kate