Can the intel SDS2 board be used without the front panel connector and
instead replaced  with the generic wiring options?

I'm guessing that you are talking about the panel that has the LEDs
for power and hard disk + power and reset button. If you are, then
here is the pin out for the Intel SDS2 board:
http://developer.intel.com/support/motherboards/server/sds2/frntpnlhead.htm
As long as a generic connector complies with the motherboard's pin out
or can be modified to comply you should have no problem.