Hi,
This is our idea and efficiently to track the Ministry pages, users, donations tracking per ministry etc..
We are going to use Magento ecommerce, the reason is we are going to use its powerful features to accommodate your requirement, so tracking, reporting is a breeze, Magento in generally allows sub domains within single installation using multivendor concept, instead vendors here it will be Ministries. So they will have there own pages and payments received through that domain will get straight into the particular account, The admin can see which ministry gets how much funds and can transfer later accordingly.
Also when payment happens typical like ecommerce site, payment receipts and invoice are sent automatically, they can also download any time using their my account.
Payment integration is easy when it comes to magento. We will also provide a widget so that they can put on there individual sites.
Let me know your thoughts.
Regards
Mouli