The issue with running the pump that way is that it will end up pulling air form the surface and then it will reduce the performance of the skimmer because the pump will loose the balance of air and water needed for the skimmer to work properly.
If you try to raise the water level of the sump to stop the pump from pulling air from the water surface, then you would be running the skimmer too deep and you would have overflow issues.
Have you considered using a sump saver skimmer? These skimmers are made for people with limited sump space where the pump is inside the skimmer body reducing the foot print of the skimmer and using up the least amount of space in your sump.
Regards,
Carlos
CoralVue