I don't have an installation of DXH connected to Sharepoint to play with, but ContentData has an ExternalTypeId property - you should be able to use this to distinguish between content that originates with Ektron versus with another system. SharePoint content, for example, should always have the same ExternalTypeId, and that value should be non-zero.
It should be fairly trivial to check this value for Ektron versus SharePoint content either by looking in the DB (last column in the dbo.content table) or by pulling one of each known type and comparing noting the values.