Penance is cheaper than flash heal, and has better HpM.
Additionally, it has a good synergy with Borrowed Time : one of the best sequence to use the buff is to cast penance, PoM, and still use it for a big slow heal (greater heal or PoH). In particular, it belongs to a very good emergency sequence : cast PW:S, then a hasted Penance if needed, and you most likely saved someone's life. You can follow with a (greater or regular) heal, on that target if needed. Or use POM, if the cd is free. Or go back to other raid healing duties.
Note that the Cata healing threads are up. The decision was made to have separate threads for Holy and Disc in an effort to keep thread lengths slightly smaller and to make it easier to find specific info.