The solution to this problem was multi - tier in nature.
Created a service reference to the target document library in SharePoint
Create an instance of the service and use windows active directory as the credentials
Use Client Side Object Model to work its magic.
Done!
var dc = new subsiteDataContext(new Uri("http://.../subsite/_vti_bin/ListData.svc"))
{
Credentials = System.Net.CredentialCache.DefaultCredentials
};
Insert your CSOM code here.