What you can do is to have a good protocol that requires no interference from middleboxes but detects it if it happens, and then a less efficient legacy fallback protocol that basically looks as much as possible like HTTPS.

Then if you detect interference from a middlebox, show the user a message that says, "WARNING: MAN IN THE MIDDLE ATTACK DETECTED. Something is modifying connections on this network. This may compromise security and performance."

Then hopefully having multiple different apps show a message like that to every user on the network will get enough users complaining to fix the middlebox so that it stops breaking new things.