small point: the author isn't saying "scripting languages aren't programming languages", nor are they saying "you cannot write programs in scripting languages" - they're saying that scripting - a particular style of program-writing - isn't programming, or put better "proper programming" which is arguably true, especially if you're writing bash or IPython scripts, where you have access to and make heavy use of shell commands.
That style of programming is very very different to regular compiled programs, and practicing one and never the other will lead to a bias, and relative incompetence in the other. This is why I'm rubbish at chaining unix commands together, because whenever I'm confronted by a problem that might need something that complex, I just use python. I have the reverse problem to the rhetorical sysadmin in the article.