Well, you can do that, or wait for ACF5 to be published as a free version, or you can modify the ACF4 files, and I don’t know how to do that. Elliot is working on getting a free version of ACF5 ready to publish and is not really making improvements to v4 any more. I know this is not a great answer.
To be honest, I just looked at the code for the relationship field in ACF4 and I don’t see why there should be any problem with adding a meta query using acf/fields/relationship/query, it could be that the problem only existed in 5 to begin with.
If you post the code for your filter maybe there’s something in it that might help and maybe we can get it working.
