Hi Ahmed,
It's the we've been running for quite a few years now. MRI is much, much faster for development, but jruby is great is a production environment, not only due to the simplicity of deployment (just a war file + sql/ddl) and speed of the production runtime, but also because it allows us to send compiled artefacts to our clients without having to divulge source code.
The only incompatibility we've found has been with nokogiri, which is just a wrapper around the native XML processors that are not quite compatible.
We've developed wrapper scripts over time that let us run things under jruby, just using the jruby-complete jar file. So we have jbundle and jrake that launch everything under jruby. Our wrappers also lock the version of jruby and the version of java, so different projects can have different jruby and java versions (this is important if you use compiled artefacts, particularly compiled gems). We use rbenv just for MRI.
Regards,
Michael