There won't be protests or rage in that form. Many aren't happy with the decision, but they understand that religiously they hold no ground here. It's a very different issue than that of the comics. Also, these 1000 year old mosques are being demolished to expand a 1400 year old mosque, not to build hotels.
It's not that everyone needs to be in it, it's that they want to. It's the second mosque built in history and holds a lot of historical significance so naturally people want to be there. Not sure why they don't incorporate those other mosques into the expansion. I'd love to do some more research for you but I can't seem to find an article that actually has their names listed :/
Regarding your last question, people don't worship mosques, they worship figures. They may worship or 'pray' to the grave of the Prophet and his companions. That's what the Saudis fear. Islam regards many places as holy but no man, woman or child is meant to be worshipped or idolized.
edit: oh wow, bounty! Forgot they existed.