Hi @bfrutchey,
Similar to the Reference Column Filter node, which we talked about in the Reference Column Filter Performance post, it looks like configuring the Joiner node also scales unnecessarily bad with wide tables (for very similar reasons, too).
Our development is talking about various performance improvements to the Joiner node these days and this is definitely an item that we shall discuss and address in an upcoming release. Thanks for bringing it to our attention. Keep it coming! 
I’ll update this post once we’ve implemented a fix.
Regards,
Marc