Data warehouse bastardization.

Help! My company, like some other companies I’ve seen, wants to build a data warehouse/data store within its 3rd party accounting system. The system (MRI) allows administrators to add fields and tables as necessary. I feel strongly that are central data store should be separate from the application data, with at most a live link to current accounting information. Does anybody have experience with expanding 3rd party application functionality, or advice on how I can convince non-database people on why this is a bad idea?