The quote sign is a legit character in a URL. That is, a valid URL can end with a quote sign character. I don't think ignoring it would be a good idea.
That's interesting. Before my previous reply I appended a quote sign in my browser's address bar (in this page) and pressed "enter", expecting it to turn into %22 in case it's not supposed to be there but the quote sign remained intact; that's why I posted my reply without checking the RFCs.
The tilde (~) is also invalid in a URL according to the RFC, but that doesn't stop everyone for using it for user names. I doubt your browser will escape that one either.
I don't think the commenting system is meant to process html. Perhaps it is a very loose regex of (http(s)?://.*)\s or whatever (sorry I didnt check to see thats valid!)