Colly, next time read the article, the first paragraph says "has been removed by YouTube, with the company claiming that the content violated the platform’s “policy against spam, scams, and commercially deceptive content” — a claim that the filmmaker behind the project is rejecting."
Wilikon, as usual is spreading media hype. There's no evidence that YouTube removed the video for any reason other than violation of their spam policy. The produce of the video is also making huge speculative accusations with zero fact to support it. The truth is that YouTube - right now - as many anti gay videso posted. If they were taking some ant-religion stance they'd remove all anti-gay, or pro-religion videos.
The bottom line is that YouTube is a business and they don't have to allow all videos on their site, for whatever reason they want. Just like people who are ant-gay can be that way and speak that way for any reason they want, like claiming "it's against my religion".
You have the freedom to hype freely... Have you watched the video in the vimeo link?