I work in a Java shop but do some statistical work using R. For me, Java is the easiest way to gather together data for an analysis. R is the clear winner over Java for doing statistical modeling. Gluing them together is possible, and some people have written bindings. However, these are not well documented, and they are not mature enough to use in a production environment. The difference when mixing together use of (J/X)* languages is that they have mature bindings (often simply because they are all written in Java).

I'm all for using the right tool for the job, but it's really hard to take on the risk of an integration one might have to maintain or expand upon. Using two languages isn't itself a problem, either for developers or managers.