The easiest way to manage colors and grayscale versions is to simply create 2 different PDF. Not only it's safer but your printer will probably also prefer this. You can probably store them in layers but that's just a risky workflow that might not save you much time.
One easy easy to replace images through Indesign is to simply create 2 different folders for your images and name the images with the same filenames. Create you color version first, save it and then create a duplicate of that file for grayscale. Then move the colored image folder and relink all your grayscale versions in that new Indesign grayscale layout, and adjust your stylesheet.
Yes, that means every time you'll make new changes to the color version, you'll either need to do this step again for the grayscale or do the revisions in the grayscale version.
But the result is far better than using the automatic grayscale conversion and you can adjust your contrasts and stylesheets properly too. There's also less risks of mistakes (eg. forgetting a layer or a spot color, etc.)