Hi Absolom,
At WHO we are using a application called Bulk Load to upload data from excel into event programs which could help you guys. This application doe not require any mapping of data elements.
The application generates templates automatically from any event program and it identifies duplicates during upload based on a set of data elements that you can define.
The latest version of this app was just release, in case it helps Bulk Load app 3.5.1 now available
GitRepo: