There is one way to make this charger, or any charger that charges through the balancing port, charge a single cell would be to make up a y-harness that allows you to connect 2 (or 3) single-cell batteries at the same time. To the charger, this would look like a 2s (or 3s) battery and it would obligingly balance charge them.
You will probably need some kind of adapter plug anyway, since your power connector off the battery, and the balancing connector are unlikely to be compatible, so when making up the adapter plug you can make it a 3 pin with 2 single cell batteries or a 4-pin for 3 single cells.
One caution I would make, though - this one has a fixed charge rate of 800 ma - so if your single cell battery is very much less than 800 mah, you would be charging at a pretty high rate. Not recommended ....