I grew up in the JW and my stand on protection has never changed since I was a kid: You don't start fights but you are allowed to finish 'em.
Concerning the situation in the OP, I would've tried to find an escape route or tried to fight back. But honestly, it's much harder than it sounds. Fighting looks easy in the movies but when you never ever fight and never consider it, it is much more difficult to gather the courage to fight back. So, even if we say: In the same position, I would have done this or that, perhaps we'd have behaved like him: scared frozen like deers in the headlights.
About the rules for self defense, in Canada, they're very similar to the Watchtower's. If someone walks in your house with a deadly weapon (baseball bat, gun, knife, crossbow, etc), you maybe allowed to harm them with the weapon of your choice. The question that will come up is: Could you flee or were you cornered and have no other choice?
If they don't carry anything, I'm not even sure you have the right to fight them out of your house. You are basically expected to call the cops and wait for them. The idea is that you are not allowed to protect material possessions. If you think about it, it's basically what the Watchtower teaches.
Honestly, I don't like that reasoning. If it were to me, it would be like the states: Stand your grounds. Your home is your safe place and you should be able to use maximum force to protect it.