using stratix II GX transceiver on low data rate..

You may set the IO pin in differential mode using LVDS IO standard in the pin assignment. LVDS can higher than 1Gbps and I think that is good enough for you.

If you must use the transceiver, you can do over sampling for low data rate. e.g, to oversample by 5 times, you send 5 1's for every logic 1 data and 5 0's for every logic 0 data. Usually people use transceiver that way is because they need to dynamically reconfigure the transceiver for multiple data rate so that the circuit can take high and low data rate.