You probably can do it in Quartus, but it will no doubt be more trouble than it's worth. You can do it in ISE, and I know it is more trouble than it's worth there.

You would have to muck about with putting constraints on signals to make sure they are not optimized away and are connected. Incidentally, do the altera tools have the equivalent of fpga editor (a la xilinx)? Reason I ask, you can also do this "connect to pin" business using fpga editor. And again, for the job of connecting a non-top level signal to the io pins this is more trouble than it's worth.
So the short answer is already given by marshallh.
