Why do internet companies prefer Java/Python for data scientist job?
So you can integrate with the rest of the code base. It seems your company uses a mix of Java and python. What are you going to do if a little corner of the site needs machine learning; pass the data around with a database, or a cache, drop to R, and so on? Why not just do it all in the same language? It's faster, cleaner, and easier to maintain.

Know any online companies that run solely on R? Neither do I...

All that said Java is the last language I'd do data science in.