The article spends an inordinate amount of time explaining that this has already happened in certain areas for other reasons, and only discusses BGP briefly (relative to the rest of the article).
It is, however, a real problem. Current protocol changes (to improve security) include a wide range of protocols: DNS-SEC, SNMP v4, SMTP (with message submission and encryption), POP3S, IMAPS, and others. Even IPv6 involves changes to increase security.
It is unfortunate that the routing backbone of the Internet is still suffering from reliability problems after all these years – even after the president said that fixing it was top priority.
The problems go beyond just security, but stability and scalability as well. Is it time for a replacement or redesign of BGP?