Given a totally free choice, my preferred language is Java - it has a very clean design and is 'just complicated enough' to solve real problems without being difficult to learn. A lot of the power is actually in the extensive and well designed libraries, which you can learn as you go along, so getting started with Java is a gentle learning curve. I think there will be a challenge to the freedom at some point in the future, and the difficulty may be where the community finds the money to fund a battle against a rich commercial adversary. On the other hand the GPL was well drafted, so I'm confident free software will come through. I don't see why business utilisation of Linux should have a negative effect.
Commercial applications can run on Linux without affecting that underlying freedom.
I think the reverse may be true, that Linux's Open Source philosophy will affect businesses. Once they embrace the idea they will start to insist on openness from their suppliers. I can see a day where many more applications will be licensed with source code. You may not be able to distribute it, but at least you will have the freedom to change and extend it for your own organisation. The reason is that they can see exactly what is going on with Linux because they have the source, and the workings of NT is hidden.