I think it would be possible to integrate migrating jailed users to/from this type of setup. My general idea is though.. Shell users like this belong in the /home directory, whereas jailed users belong much closer to the website.
Maybe it is a option then to have two types of shell users by adding a switch in the shell user options like "website shell user" and "general shell user" or however we would name then. So a admin can add shell users with access to the website then and additionally have shell users in /home/... for shell or development tasks. So we dont have to touch the current shell user system and just implement a second type of users which dont interfere with the current setup.