First, thumbs-up on Boinx iStopMotion. Very fun software. As far as your question, if you’re capturing the still at their maximum bit depth, that’s all you can do… but maybe it’s not a waste, because once you’re operating in prores 422, at least you’re not losing any more… and the potential for editing with more layers and effects in FCPX or Prem Pro or whatever is better if you can operate in prores. IStopMotion is very good for the price point, if you’re concerned about higher quality, then maybe ToonBoom or something more higher-end is really what you’re wanting.
That said, when people ask me what software is best, I say: “the one you like the most”. because, if you like it, you spend more and more time with it, and that leads to mastery and efficiency and an output that will rival whatever the competition is. If the interface is intuitve for you, and you like the workflow, Keep going.
One idea that comes to mind is, you probably have photoshop. PS can run batch actions on your grabs and convert them to tiff or other formats. It won’t add resolution or detail that wasn’t there before, of course. But if you need the stills to be upscaled, so you can do more synthetic pans and zooms and croppings in a video edit, that might be an option. Apple Compressor and a few others can also do that.