Interesting theory, however, it is false for these reasons:
- Order 66 is to exterminate Jedi. Why would they kill Republic troops?
- The Republic hasn't even landed on Kashyyyk yet when Sev is lost. Remember, you see at the end all the Republic Assault Ships invading?
- Order 66 isn't issued until later on in the battle.
- The advisor is giving orders from Yoda which for sure means Order 66 isn't out yet.
- It is droids that capture him. If you listen carefully you can hear Droidekas firing.