Logging the forests makes sense. I've worked with wetlands conservation, and to save the wetlands species (orchids and pitcher plants, to name a few) we cut down and burn hardwoods.
In Virginia, we have an endangered woodpecker called the red cockaded woodpecker. It only nests in certain species of pines. These are fire reliant, so the area is burned when other trees start taking over. The spotted owl could be like this, only nesting in select trees.
This does seem like it's interfering with natural selection a bit, but I don't know the full situation. The barred owls could be getting pushed out of their native range by human activity, thus invading spotted owl territory. I'd have to read more on the situation to weigh in fully on it.