I'm not sure about the bacteria, I'll let a foodsafe person chime in on that. I have encountered a similar problem when after quite a few hours the fish is not done, I am tired and ready for bed. This happens mostly on colder days. With a little chief I like to allow 12 hours to finish the product in the smoker.
I have on a few occasions finished the fish off on the BBQ at low temps. The smoking part is done in the first few hours, you just need to finish the drying process. The BBQ does a good job of that.
Another way to do it is to increase the heat in the smoker. You can put the box of the smoker over the smoker and that helps to keep the heat in. My Brother sometimes throws an old sleeping bag or the likes over the smoker to keep the heat in as well.