Joe, basically you've run into input that's not easily scriptable. Having to provide interactive input defeats the purpose of automation, anyway-- you might as well log onto the box with ssh at that point.
I would say see if expect does what you need to do. If it's even more complicated than that, I would test the program for the "tree" of answers to give, then determine which trees you can have a script follow, and write one (in some kind of high level scripting language like python or ruby).
If those alternatives don't pan out, it's time to look at what other tool besides this interactive command line utility could provide the same functionality
What does this thing requiring interactive input do?
Moses