As long as the imaging device you use is capable of creating the quality of scans you want, I don't see how changing the device you use to create the scan would be a problem.
There are some things to check and to consider in order to make sure that happens, of course. I would personally double-check that the optical resolution of the cheaper desktop scanners (not the interpolated resolution) is sufficient to meet your resolution requirements, and that the camera set-up will give you the kinds of images you're looking for (e.g., resolution, lighting, camera stand, etc.).
The bigger concern (in my opinion) is all of the administrative questions that need to be answered: Are you able to organize and preserve these new outputs in a way that is consistent with (or part of) your existing procedures? How will you decide what bypasses the existing procedures? Who will be responsible for this new scanning? What are the cost implications? How will you provide access to the files? Would it be better to improve the current workflow instead of adding a new one?
Hope that helps!