I live in the area and, my my it's a touchy thing to wade into...But a few points:
-I think the main issue is typical NIMBYism about towers and the Muslim aspect is a crucial subtext. I think they'd be griping about any towers of that height (which, right on the main street, don't seem crazy to me) but the fact that it's the mosque is just amplifying everything.
-Thornhill itself (at least much of the development along Bathurst) was designed to appeal to the Jewish community so unless they were illegally banning non-Muslims, it seems a bit hypocritical to me to say "we don't want some monocultural group developing our area!" If they're somehow spinning it as "Muslims-only," that's different but I didn't really get that impression. As for the legal ramifications, interestingly, they are allowed to restrict ownership if they are affordable units. That might be an issue in the seniors facility, but I don't think they could do it for the condos.
http://www.yorkregion.com/news-story/1469434-human-rights-commission-backs-region-s-decision/
-The mosque (and a nearby jewish school) have been there a long time and co-existed just fine. Yes, Muslims and Jews don't always get along and yes, there was that incident (cited above) where the mosque was found to have some, ahem, not-Jew-friendly textbooks but I think blowing this up into an actual potential
threat is absurd.
-The JDL are not my cup of tea and their involvement is likely to make things worse but "radical terrorist organization" is a bit much. If that's how you describe a few guys stirring up crap at a Vaughan council meeting I'm curious what language you use for Al Qaeda and the PLO and, you know, I hate to mention it but I guess they're Muslims, FWIW. I know that's the terminology that website uses but Kahane has been dead a while and they're not active in that regard.
It's unfortunate that the religious aspect is getting people fired up (it's also why the media are covering it, of course) but I think it's mostly generic NIMBYism at work. Heck, in one of those news clips there was a guy from "The Association to Preserve Thornhill Woods." To preserve their subdivision which is so new that if you look at Google Maps, it's not even fully built out in the satellite shot. So, it's a fairly absurd discussion at this point. Hopefully that will change as it moves through the process.