One other thought: we know that the Klingons were preparing to board the ship, but it wasn't clear exactly when that would happen. Kirk had surrendered and was willing to let them come aboard, but he couldn't have known that they would wait until the agreed-upon time before beaming over.
Whatever happened, McCoy's survival was absolutely necessary, so he could not have been on the ship when it was destroyed. That's why Kirk sent him to the transporter room first rather than having him wait on the bridge. Had the Klingons decided to board the ship sooner than expected, McCoy would not have been able to defend himself against Kruge's men. Sulu was only one person, but he had extensive hand-to-hand combat experience and could have defended McCoy long enough for him to get off the ship.