You can change what System.out and System.err actually refer to by using System.setOut and System.setErr. However, you would need to find a good alternative for the PrintStream for these methods. I'm not sure it will be easy to get hold of the RollingFileAppender's internal streams. Furthermore, you would need to reset System.out and System.err every time the appender performs a "roll", because it will get different streams (closing the old ones, opening new ones).
I was keeping mum until someone suggested something simple and obvious. But that's about as close as I could come myself.
You should (theoretically) be able to replace the System.out and System.err values with alternative OutputStreams that funnel themselves into code that writes the text lines into a log via whatever logging interface (juli, log4j, whatever) you like.
Regardless, a library in this day and age that is so brutal isn't well-designed. I'd recommend looking for a more civilized equivalent.
Sometimes the only way things ever got fixed is because people became uncomfortable.