Early in its life, JRuby+Truffle was a separate project and its goal was to run everything MRI can. Thanks to efforts on both the JRuby and Oracle sides, the project was open-sourced and merged with JRuby. That brought along a ton of benefits for us, but did open the JRuby ext. can of worms.
I'm trying hard to answer your question without committing to solve a problem we haven't looked at in depth. I suspect we'll wind up supporting some portion of the JRuby ext. API, but whether that ends up via an alternative implementation, a sandboxed JRuby runtime, a bytecode processor using something like a hypothetical TruffleJava, or something entirely different, I don't know. We've had enough pure Ruby code to try to get working that we've been able to defer the extension discussion for a bit.
Having said all that, to really get the benefits of JRuby+Truffle you're going to want to use Graal. While JEP 243 [1] should make deployment scenarios much easier starting with Java 9, you'll probably still need to coordinate with your ops team since the JAR needs to be on the bootclasspath. That's really just to say that you won't be able to just drop the JRuby JAR in and get optimal performance -- there's still going to be a second step that you might not be able to "backdoor" into your stack.