Hello Carlos,
unless you did tests over an extended period of time my guess is that when you did the first test one link on the path was experiencing congestion.
When you see a so high delay this means there is congestion unless you are using satellite links
You are not pinging the supervisor if my understanding is correct, so these packets are processed just as standard user traffic.
What is the link between the two C7609 ? What linecard or service card (SIP or other flexwan)?
unless it is a WS-6708 or WS 6716 that has a DFC 3C onboard that matches with PFC 3C on RSP 720 3C ,there is no other difference
what was the IOS image used on the sup720?
Likely the RSP 720 is running a newer IOS image.
So generally speaking the answers to your questions are negative.
the RSP 720 can improve routing convergence on learning BGP full tables thanks to its MSFC4 that is better then MSFC3 in sup 720.
A possible difference can be the number of IP prefixes that can be handled by older sup 720 3B and RSP 720 3C but I think they both support 256,000 routes
see datasheet
http://www.cisco.com/en/US/prod/collateral/routers/ps368/product_data_sheet0900aecd8057f3b6.html
http://www.cisco.com/en/US/prod/collateral/switches/ps5718/ps708/product_data_sheet09186a0080159856.html
Hope to help
Giuseppe