From what I read, but didn't try it, Procera PaquetLogic is one of the most popular solution for WISP.
Since the ePMP do a faire sharing between user, your main concern should be backhaul. Anyway, it would cost too much to had a DPI device at each customer. By hadding a DPI box in each tower, you had QoS to backhaul and also to customer download since the DPI box would be hit before the customer is reach.
nDPI from ntop is use by Ubnt on the EdgeRouter. I'm not impressed by the result in finding kind of traffic but it could help a little. The EdgeRouter don't support offload for adding DSCP value to paquets. but you could use it on probably any *nix device powerful enough.
Mikrotik have a L7 functionnality that could maybe work better (didn't try it yet).
http://wiki.mikrotik.com/wiki/Manual:IP/Firewall/L7