"Defending the Watchtower" happens well after the beholder's been defeated. By defeating the beholder, the group has freed the watchtower from the Far Realm, and it returns to the world.
The characters should report to Padraig that the watchtower has been retaken, and it is ready to be inhabited. Padraig will send mercenaries to use the tower to start watching over the King's Road so that supply caravans can start making their way to Winterhaven again.
Now, the tower defense can come about in a number of ways, but the two that are, in my opinion, easiest are:
1) The orcs from the village have finally noticed that their incursions are being stopped. Orc scouts finally made it through the Feygrove (or went around the long way) and noticed that soldiers are now in the watchtower. Bakrosh has sent a major force to take it for his own use.
2) If Bakrosh is defeated, and the orcs are pushed out of the village already, then perhaps the orcs, in a desperate last bid for survival, have started an assault on the tower, hoping to take it back. If they succeed, it will be both a major blow to the region's inhabitants and a great boost to the orcs' morale. If they fail, then the Vile Rune orcs may very well be lost forever.
edit: Remember that the encounters are numbered for ease of reference. They're not necessarily meant to go in order, or even sequentially. So, you might get the tower done somewhat early, but then the players will move on. Later, near the end of the module (because that combat in Defending the Watchtower is pretty hard due to the high-level giant), the actual defense of the tower will take place.
