I could easily see making <script> and <link> resources required to be separately requested (like images are now -- ignoring data/base64 resources), but we're back to redefining HTML.
I'm not arguing against that...
It's really hard to have these types of debates though, because everyone focuses on different problems of the HTTP/HTML webapp request/response cycle. Like you said, adding separate control/data channels would help, but that doesn't solve SQL injection attacks (which is a whole other class, but that's not really an HTTP/HTML issue, it's a backend issue and I don't see how you'd avoid that with a simple protocol change). Simply making HTTP stateful could potentially solve a different class of session highjacking, etc...
There are so many attack vectors that I think it does make sense to think about what a replacement for HTTP/HTML would look like. Most of these problems arise from trying to re-engineer a document format (HTML) to support interactive webapps. We should think about how to do this better... (without recreating ActiveX -- shudder).