First off I would say more power to it. I think this is great if this is what it takes for the project to continue. Clearly using Ubuntu as a base is not perfect for all projects, so it makes sense to use the tools that best meet the needs of the developers.
As long as the hardware detection is present, including Wi-Fi, I cannot see anyone having any issues at all with the switch from Ubuntu to Debian for the Eeebuntu project.
From here out, the real question is likely to be the next name for the project. As clearly sticking with the existing name is likely dancing on the trademark issue a bit too closely, there have been those who have suggested going with something like Deeebian or Eeebian. In either case, both would be fitting names for the switch.