If I had to guess, I'd say "beating" him would just skip it right to the same result you get after waiting around for a while. Other "undefeatable" enemies in the game, such as the battle with Ozzie in Magus' castle, do not really show any special result when you defeat them. I had Robo crush Ozzie in one move with the Armageddon Arm, and it merely made it so I couldn't select Ozzie as a target on any of my character's turns after that; I could only attack the cranks. Then again, that situation is probably different, since there were other targets to hit in that battle, whereas in the Cyrus battle, there is only Cyrus. I think you should go for it. Let us know how it turns out!
