This is the reality of making the toolset drive the database and not the other way around. You sound like you are in the position where you need a compreshensive database structure, one that you can derive reports, create updates, publish maps, etc. with or without the GIS part. Freeing the data from the tool will give you the ability to use an appropriate tool of your choosing. That is why we have Open Standards. From there you can use the application that best serves the purpose you have in mind. I just had this conversation this morning that if you happen to represent data in Columns it doesn't make it an Excel Spreadsheet.
Another responder discussed the limitation of Python, this is not so. There is probably more things you can do with python due to the extensive libraries then most any other language, and interfaces are not that hard. What is limiting is ESRI's implementation of Python in ArcGIS. Dont confuse the two.