I second that. R is terribly useful for the wide variety of libraries available and esoteric statistical procedures. But you would *never* want to write a long/complex program in R.
As you say, it's most convenient to work in some other language that's actually designed to be scaleable, object-oriented, and easy to debug. It's usually straightforward to call R libraries when you need them. I find that python+scipy+rpy is an almost ideal environment for day to day scientific programming.