With work, I expect that any Gimp process can be replicated in ImageMagick, though it might need C code.
If the Gimp process gives a good result, I would simply use Gimp. Gimp can edit images non-interactively. (At least, it used to be able to. I haven’t tried this recently.) So it could batch-process the images.
IM’s common downsampler is “-resize”, which has infinite varieties, using “-filter”. Most people want to add sharpness, but I expect some varieties will do the opposite.
If noise is a problem, I would treat that as a separate issue to downsampling. Denoise first, then downsample. Different types of noise need different treatment. Maybe a simple blur to remove or reduce high-frequency data. This will also blur edges, which I guess doesn’t matter here.
I’m currently playing with techniques that limit outliers. For example, calculate the mean and standard deviation in a small area around every pixel. If the pixel is outside the range (mean +/- k* std_dev), cap it to be within that range.
But will noise be a problem when scanning orange peel? I don’t know.