"In the early days of the Internet design, my officemate at MIT, Steven T. Kent, who is now far more well known as one of the premier experts on secure and trustworthy systems, described how the Internet design could in fact, be designed so that all of the bits delivered from source to destination were encrypted with keys unknown to the intermediate nodes, and we jointly proposed that this be strongly promoted for all users of the Internet. While this proposal was not accepted, because encryption was thought to be too expensive to require for every use, the protocol design of TCP and all other standard protocols have carefully preserved the distinctions needed so that end-to-end encryption can be used. That forces the design to not depend in any way on the content, since encryption means that no one other than the source or destination can possibly understand the meaning of the bits, so the network must be able to do perfectly correct job without knowing same."
Key and cipher negotiation could easily be shoehorned into the three-way-handshake already used to establish connections. AES with a CTR block mode would be the obvious cipher choice since each packet would be handled separately. With TCP you could even just use the sequence number as the counter, although this would be harder at the IP layer.
But yeah, none of this would have been available at the time. Still, given today's technology it would not be difficult to future-proof, especially if the trust machinery is left to the application.
Start with AES-CTR (which wouldn't have been an option in 1979; counter mode hadn't been invented): you can't use TCP sequence numbers as counters; among other things, multiple segments can be sent with the same sequence number, and while the byte described at the stream offset of those sequence number (usually, but not always) agrees with every other packet, no other guarantee exists about the nature of those segments. Reuse of a counter in CTR mode is a devastating flaw.
Running DH over an unsecured connection with no previous trust anchor is also a recipe for disaster; attackers don't even need a fully-functioning man-in-the-middle to break it; they just need to be able to inject two segments, one in each direction, to fixate the derived key.
Everything else you propose to layer on top of this DH + AES-CTR connection is handwaving; if you have to run "application-layer" TLS, what's the value of hardcoding (broken) crypto into the TCP layer?
Sorry for the rabid response to a well-intentioned comment, but wow I couldn't disagree with you more strongly.