I drain them, set them in the sun for a day or two, making sure there isn't any water left in it by periodically turning the jug over so any last drops get spread around the inside and evaporate. I always give the jug a good rinse before filling for a trip. If you only put clean water into the jug, & then dry it out after use, there shouldn't be any trouble. Dessication and backyard sitting-in-the-sun heat will do a pretty good job on any protozoa and bacteria hanging out in the jug.
Never had any problem, you may be overthinking this stuff or watching too many Lysol commercials.
If you're really worried, give it a good bleach rinse before
you use it. That's when you want it clean.