Yes JVMCI can help there in a couple of areas. Part of Graal (the new compiler) is a new FFI that bypasses JNI and can represent native calls directly in the JIT. That should improve native call performance.
There is also a C interpreter with JIT being built on top of Graal and JVMCI. In JRuby we're looking at interpreting C extensions rather than running them as native code. In some cases this is faster than the native code, because we can optimise the Ruby and the C code together.