The way it seems now, neither the two Kenpachi's, nor any other captains are at a level where they can stand a chance of surviving another onslaught from the Quincies, especially after seeing Yama get slaughtered in BK mode.
Apparently, for Zaraki to be of any benefit in the upcoming battle, he needs ascend to the next level, which will happen only after he's pushed to the brink of death repeatedly(and possibly learn BK in the process). I'm thinking once he reaches that power level, he will be far beyond that of even Unohana, and it will give them a better chance at survival. With both of them going all out, she might end up as collateral damage although I'm not so sure. Like you said, it would be a huge waste to kill either of them off.
After a couple of chapters, I see a newly powered up Zaraki ascending from Mugen carrying the limp almost lifeless body of Unohana over his shoulder, where she will then be taken to her squads barracks to be healed back up.( I really hope so anyway)