I couldn't articulate it nearly as well, but that's pretty much my reading of the Gardener/God Garden plot line too.
It's probable that it's the last we'll see of either of them this side of Convergence, but I very much doubt it's the last we'll see of them ever. The Gardener's lost her "son" and active agent, with Midnighter departing. She's going to need another, and she might well try to offer Dick the job. He may even take it on a temporary basis, if her goals run parallel to his own.
Plus, she's got the ability to negate his hypnos tech, and he badly needs that to safeguard himself against hostile elements within Spyral. Maybe they'll do a deal at some point, and she'll help him out if he helps her.
Is Midnighter gone too? From the God Garden, yes. From the current story arc, maybe not. It all depends on what happens with the Paragon parts once the full set (-1) has been collected. Maybe he'll intervene again then, but as a private agent this time.
And it does occur to me that at some point Midnighter is going to discover that Dick is still working with/for Batman, and that he's got his motives all wrong. But if by the time he finds that out, Dick is/has been working with the Gardener, he might still disapprove of him with the same seething passion that he currently does. It opens the possibility that they could continue as antagonists. Though I think Dick has pretty much exhausted his surprises if it comes to a fight. He'd probably never come that close to forcing a draw again.