Just FYI, by default, you won't be able to stop the SEP service through Services console. The service can be stopped only by executing the "smc -stop" command in "Run". However, you don't need to manually stop the SEP service to deploy the communication package from a SEPM.
If the remote deployment of the communication update package fails, try saving the communication package and copy it to one of the clients in site2 and (after unzipping) manually execute the sylinkdrop.exe and chec if that works.