Hello,
Unfortunately, I am afraid that this won't work. A router will generate NetFlow records only for traffic that is in fact being routed by it. If you just connect a router to a SPAN egress interface, the router will not even bother looking at the traffic because the destination MAC addresses will not match the MAC address of the router's interface.
I am afraid that you would need a different solution. There are some OpenSource-based solutions that can run on dedicated hosts connected to SPAN egress interfaces, such as nProbe:
http://www.ntop.org/products/netflow/nprobe/
I am sure there are also commercial solutions available, but truth be told, I have not tried any myself, so I cannot provide a first-hand experience.
Best regards,
Peter