AFAIK lack of net neutrality could greatly affect the Safe network. Without net neutrality there would be nothing to the ISP doing deep packet inspection and severely throttling or just blocking all unknown protocol encrypted traffic. They will just block it and see who complains. “Sorry, only encrypted traffic using authorised certificate authorities (compromised) certs are allowed on our network - to stop terrorists communicating of course.”.
That is why I think pluggable transports for protocol obfuscation like Tor uses (for example where Safe net traffic can appear to be skype or some other suitable “ISP approved” protocol) will become a natural extension and necessity for this project.