Strictly speaking, yes, they CAN do this because the EULA for the CS and GECK allows them to.
EULAs aren't everything. If a mod was made just using the Construction Set, then Bethesda might be able to make an argument (probably not though). If the modder has created things outside the construction set (textures/models/etc) then Bethesda wouldn't have a leg to stand on legally. The fact is that mods contain the creative work of the modder, and no EULA can give Bethesda complete rights over that.
