This is now supported via the --configscript option.
Just create a config script (e.g. conf.groovy) like this:
Then call with something like:
groovyc --configscript conf.groovy -j MyJava.java MyGroovy.groovy
While it would be possible to try to emulate this with separate individual switches, it becomes cumbersome to try to support options in a generic way (allowing more to be added easily) while also providing rich typing (e.g. keepStubs and stubDir are Boolean and File rather than just Strings)