Synergy 2.1 will roll out as a beta in January and a final in later months from January. That will include an offline activation and connection service. v2.0 was made primarily to address auto-configuration. If your internet is down, establishing a new connection will not work, but your connection is still local, making the lack of an internet connection a non-factor.
All the cloud is doing is bridging the two computers by sharing IP info. After that, the connection is purely local and no longer dependent on the cloud. That's the flow I got from Nick, and if it isn't this way in v2.0, it