Counter flow chillers are great and I made one. Sanitation should not be a concern if you clean when done and sanitize prior to use.
When I'm done brewing I run hot water through the line and drain. When I'm ready to use next time I will run star San through first and then let a little hot wort through before turning on the cold water and running into kettle, no infections reported here
BTW I use a gravity set up and not works great!