If the problem is "new server won't use hashagg", I'd wonder whether the work_mem setting is the same, or whether maybe you need to bump it up some (the planner's estimate of how big the hashtable would be might have changed a bit).
I actually was speaking with Stephen Frost in the slack channel, and tested both of those theories.
The work_mem was the same between the two servers (12MB), but he suggested I play around with it. I tried 4MB, 20MB, and 128MB. There was no difference from 12MB with any of them.
I have my default_statistics_target set to 300, and ran a VACUUM ANALYZE right after the upgrade to 9.6.1. He suggested I lower it, so I put it back down to 100, ran a VACUUM ANALYZE, and observed no change in query. I also tried going the other way and set it to 1000, VACUUM ANALYZE, and again, no difference to query.
