I believe they will. I have not tried with different versions of the OS. But, I have succeeded with a 5.1.2 server running freeswan 1.9.3 making a connection to another 5.1.2 server running 1.9.7.
I have also created VPNs between freeswan and Cisco PIX and Watchgurad products too.
In theory it should work.
Hope this helps..
-James