There is, and always will be, a point at which you have to say "I've stopped working on the 'negative' and am now working on the 'print'". Even if you could, in some sense, do completely non-destructive pixel cloning or pixel synthesis (healing) all the way through the process, your cloning/healing source might no longer be appropriate after you've made adjustments to the underlying image.
That said, Adobe Camera Raw, Lightroom and Capture One Pro all have at least basic spot removal tools (more like the healing brush than the clone stamp) that will allow you to get most of the heavy lifting done on the "negative" (provided that you're using a reasonably current version, of course). Those tools work at the raw image file level, and are applied before adjustments are carried out. No, they're not as precise as your subsequent work in Photoshop can be, but that shouldn't matter: you should be well inside the ballpark with your major adjustments long before you go off diving into details. That includes things like multiple developments, which you might orchestrate from inside of Photoshop using Smart Objects (to rescue textures, to fix or fake mixed lighting, and so forth). If you sand, stain and finish your rough lumber before you decide what you're going to build, don't be surprised if the sawing, drilling and routing messes that up a bit.
Once you're in the right ballpark, you shouldn't need to go back to ACR (or what have you) again; adjustment layers within Photoshop can reasonably large adjustments over top of your retouching work. No, they can't adequately manage a 2500K shift in colour temperature or rescue clipped highlights and shadows¹, but you shouldn't be doing pixel-level work on a picture you're not even sure can "work" yet. If you've spent four hours perfecting the silky fur on your glorious, world-beating cat picture before deciding that the image is two stops underexposed, the highlights over there are blown, the noise is unbearable, and the cat probably wasn't purple after all, then it's time to re-examine your process.
If the picture is roughly right and nothing important is clipped in the base image data, then there's little you can't do with adjustment layers over top of your detail work. Just remember to do all of that work beneath your "final touch" colour and contrast adjustments.
¹ If you're working in 16-bit mode, you can actually shift colours and tones quite a bit with virtually no penalty, provided that the data are there. It's not as simple as using the sliders in your Raw converter, and often involves individual colour curves, but there's a lot of power there nonetheless. Clipping, however, is forever.