You can still re-activate the civilian skills, and the off-duty soldiers will still perform the labors - though they'll lose the settings again next time they're activated (I don't recall if it has to be a manual squad order, or if scheduled orders trigger it too).
While it's got its downsides, seems nicer than 40d to me, since there if you left a quality crafter in the military too long there was no way to get that crafter back. Here, you can always 'correct' a mistake (or change a decision), though the UI keeps 'hybrid' military-civilian individuals more micro-manage-y (mostly from this labor resetting, or from the equipment management if you remove them from their squad). I do miss the 40d insta-draft, though.
You can still eventually 'forget' about managing the military personnel, in a fashion. They eventually reach a point where they no longer complain about long on-duty periods (I *think* that's the same point where they start resetting their labors, though I'm not certain), so you can just keep them going eternally (and hope they actually *drink* the alcohol in their flasks for once ...). And if you keep them perpetually active in the military, then you don't need to worry about the decay of their civilian skills and the associated bad thoughts from being deactivated without a novice+ civilian skill. Not quite 40d's low-military-management, but reasonably close imo - just takes a while to get there.
iirc, this is labor reset is in the bugtracker as a bug, so there's a chance it will be fixed eventually.