It is not true that Rails 3 is dependent on Prototype.js. It is just that it is what Rails started with. You cannot just get rid of something that will break backward-compatibility.
Btw, Rails 3.1 will start supporting jQuery. https://github.com/rails/rails/commit/708e09448ba41c45f189c6...
That's a commit of mine. But, it won't be in the official release of any 3.0.X. It is currently only on the master trunk and soon it will be released together with Rails 3.1.
To answer your second question, I don't think that anyone in the Rails community will say that SC is the future of Rails 3 even though two of the core contributors of Rails are involved in SC.
And, don't forget that 37 Signals which is the company started Rails is going to release their Cinco javascript framework.