If the inline filter is used at the same rate as the under-sink filter then I would think that it too would have similar bacteria. Don't know about you but when I put away my in-line filter it has water in it. My RV also has a whole system water filter as well and that also has water in it. When I hook up at a campsite I let the water run for a minute and then that is it. Have not had any ill effects so far. For drinking we have a Brita jug so the water flows through the aforementioned 2 filters before it goes into the Brita and is consumed.
Moral of story - I wouldn't bother with the bacteria. Leave the filter where it is and enjoy camping!