If I had a guard dog who I trained to attack intruders, would that be considered booby trapping?

Good question, honestly. But no. That's a whole different set of laws.

Do the same threats not exist in that scenario for uninvited guests?

Depends what you plan to use for a hypothetical booby trap.

My argument is that any innocent person should be legally allowed to defend themselves and their property.

And I agree with you on that. I'm a proponent of castle doctrine (to a point), but it doesn't account for booby traps.

If they accidentally hurt another innocent, then charge them with that.

That's what the current booby trap laws already do. They aren't meant to protect criminals, rather it's to protect innocent people who stumble onto said booby traps.