To be fair, the article doesn't say Google "secretly wants" downloaders to work. It says they need downloaders to work, despite wanting to make them as annoying as possible to use. The argument isn't so much about Google's feelings as it is about whether the entire internet would continue making YouTube the video hosting site to use if downloaders were actually (effectively) blocked.
I don’t think companies are asking “can people download this video” but rather “can people watch this video” - downloaders seems like an afterthought or non issue.