Mathematica by default uses its own ssh implementation. You can see it in the dialog of the remote kernel configuration dialog in the advanced options:
`java` -jar `mathssh`. As far as I know, you can safely replace that with the local ssh command (most likely
/usr/bin/ssh). You have to select the "Advanced Options" radiobutton to do that (if you first add all the standard options, the rest of the command is already filled in correctly).
Edit: By default, Mathematica uses the launch command
`java` -jar "`mathssh`" user@hostname math -mathlink
-LinkMode Connect -LinkProtocol TCPIP -LinkName "`linkname`"
to invoke ssh, where
hostname are filled in via text boxes above. To use the local ssh command, you need to change the above command to
ssh user@hostname "math -mathlink -LinkMode Connect -LinkProtocol TCPIP
-LinkName `linkname` -LinkHost `ipaddress`"
This appears to have one flaw, killing the remote kernel via the front-end no longer kills the processes on the remote server. So, that will have to be done by hand.