What I mean by this is: I have two separate save files with Kinu in them. Will I be able to get the "Goddess Of The Grain" achievement for raising the Inari in one save file while having the Kitsune in another?
Yes. Steam achievements are unlocked globally: it doesn't matter if it's your first playthrough or your hundredth, or whether or not you've taken any mutually exclusive options in a previous playthrough. In fact, a lot of games where player choices have significant impact will have achievements for mutually-exclusive paths, to encourage/reward multiple playthroughs with different options taken in each.