The biggest issues would probably be software, speed and allowance for hysteresis in the scan coils. Taking those in reverse order, I know even our JEOL 840 can be significantly off at high scan speeds, but normal active digital scanning systems will probably not be near that fast. There can be a significant amount of overhead in stepping from point to point so that scans can be slow for 1024 pixels across the image. We find 100 us of dwell per point is plenty from a signal standpoint. I don't know how fast the scanning can reasonably be performed in conjuction with image digitization.
Software is a non-trivial issue.
Being a tinkerer, I could probably come up with a hardware solution in a reasonable amount of time. However, the software will probably determine the overall satisfaction with such a system. It is probably the greater investment of energy. FWIW, we are happily using the Quartz PCI passive imaging system. Rather than taking over control of the beam, the system passively monitors the scan and records the image.