Not all users have the expertise to figure out that there is a direct link on your torrent that they can use in their browse or web manager. Maybe they "have the right" to use your web server. ;) Anyway, for must users it would be wiser to use torrent plus your direct link peer for the best download.
Anyway, I am trying to figure out what is your motivation to do this, I think you would get better advice if you explain this. I imagine it is bandwidth. What you could possibly do is to restrict the User-Agent in your web server so they can only work with certain clients, but others would be impacted or you could throttle your web server with certain parameters.