I would like to wrap a few block tags in a link (valid in HTML5):
foo
bar
At the moment CKEditor (4.2) is xHTML/HTML4 editor only. There's no support support for HTML5 DTD (which is dynamic, BTW) and this is the root of your problem. I'm also afraid there's no workaround/config since different DTD means different parser, so CKEditor is not the right tool for you. Sorry.
You can find more information in this ticket.