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.
You can try doing something similar to this:
CKEDITOR.dtd.a.div = 1;
CKEDITOR.dtd.a.p = 1;
src: http://ckeditor.com/forums/Support/CKEditor-wont-allow-inside