Ninja
Changing to a Ubuntu server is out of the question. I have many years of hosting and dozens of websites tied to this server, and the last thing I want to do is reconfigure it from scratch.
After reading up on the differences between CentOS and Ubuntu as web servers, CentOS is highly regarded for business use due to its higher levels of security. The ease of making changes to Ubuntu servers comes at a price of lesser security.
There must be others running FFMPEG and JS successfully on CentOS servers. It would also seem to me that a high level company such as yours would have someone in your staff with the ability to fix this issue. I have given you root SSH access, what else would you need? It's not like CentOS is that rare, in fact it has a very large install base.
And here's another thought... I did some research and this issue of video processing seems fairly prevalent among JS users. Is there not a way you could offer a paid service to process videos for your clients? It seems fairly simple to set up a portal that could do such a thing, and taking the hassle away from your clients is surely something that many of us would pay a little extra for.
Sorry, but I'm really disappointed by this situation. My client needs this functionality for his livelihood.