Hey Joseph,
Thanks for the post and sorry for the delay in getting you an answer. I've been trying to track down someone to figure out what is going on, but we are a bit stumped at the moment. The Java SDK should still respect goOffline(), but clearly something is amiss. We are tracking this internally and are going to try to repro this to figure out what is going on.
In the meantime, can you try using the new Firebase Admin Java SDK (latest version as of this comment is 4.0.1) and see if you can repro the same thing? I have a feeling it will have the same issue since I'm not aware of any changes though would have fixed this. But still worth the shot. Side warning: it is a known issue that the Admin Java SDK currently doesn't work in Java 7.
Also, if you could provide us with anything else to help us repro, we would very much appreciate it. For example, is there a minimal repro you can share which exhibits this behavior? Are you using Google App Engine standard or flexible? Are you running on Java 7 or Java 8? Etc.
Hopefully we can get to the bottom of this.
Cheers,
Jacob