A shot in the dark but maybe implement a wrapper for the protocol in something that looks more like http? Websockets perhaps? Otherwise I think you will have to build your own countermeasures specific to your protocol.
The blog post does mention this possibility. In a similar vein we can also try to mimic a protocol that is well supported by hosters, like source or minecraft but I'm fairly certain that would be the single most ugliest piece of code ever written :)