In a synchronous rectifier, current will flow from source to drain, correct. There's nothing wrong with that.
You should keep in mind that using synch rectification for a flyback will probably not give any significant benefit, especially if your output voltage isn't very very low. However, it will likely be expensive to implement (since it requires gate drive with isolation). Synch rectification should be reserved for lower output voltages, and more efficient, higher power topologies.