Here is another design.
With this design, the pump would be on the output side. With vacuum in the output pipe, the light blue tube rising from the output pipe "should" allow air to escape. Even when the pump is off, the filter should purge enough to prime the pump. I doubt it would purge 100% on its own though. Although it would be a cool idea to play with, with some small pipe and tubing and a sealable container.
With this idea though, there will be a tiny bit of bypass using 1/8" or 3/16" solid tubing but nothing that would be noticeable.