Sooo....reporting back.
I wasn't sure where we 'merged' together to do the customs stuff together at the machine, so I just went down the US citizens line and him down the visitors line. This ended up splitting us completely, but it didn't really matter, I thought. When my husband got up to the counter, the agent sent somebody to get me (I was at one of the machines), as they wanted us to go through together - so I was processed with him at the visitors counter. There was literally not another passenger at all yet in the immigration area, so we were through it in about 2 seconds.
On the way back we went via Atlanta, and here the queues were HUGE. I asked the guy directing people to different lines if my husband could join me in the US citizens queue, and I was told yes (though from looking at the signs, it seems any returning ESTA person can use the US citizens line - and thus it wasn't a perk of being married to a US citizen? Surely not, as then nearly everyone, US and foreign, could use it?). Anyway, the machine was able to process us fine together, and we went up to the counter together without any issues.
Nobody batted an eye either at the same-sex couple thing (I asked a couple other people while queueing to make sure he could be in the line with me, to not have to queue again when we finally got up to a machine.)
Also pleasantly surprised with ITI baggage transfers at ATL meaning we didn't have to pick up our suitcases. At JFK everyone had to fill out a paper customs form but on the ATL-bound flight, they said no US citizen or returning ESTA holder had to fill a paper one. So very different processes at both airports, it seems.