Sharepoint: How to survive after the first deployment on Prod

I have encountered a main problem with update the existing site which was created from custom site definition. It's almost impossible to guarantee that site will survive in case something is changed in the list schema.
It's worth to notice - that described method above is not supported by Microsoft:

Supported and unsupported scenarios for working with custom site definitions and custom area definitions in SharePoint 2003, 2007 and 2010

 Here is a helpful terminology about the site definition and site template

Creating, deploying and updating custom site definitions

And finally as a "panacea" for all this deployment hell :feature stapling
The real example how I use it here

In essence, you can't deploy a new list schema (ex. remove some fields, change type for existing fields) over already deployed site. The only way to do it -through object model.

Here is the additional tips about the object model pitfalls:
Additional tips about Sharepoint API

Just found old and "unsupported" msdn article which cast the light about difficulties of sharepoint redeployment:
Adding Functionality That Affects the Existing Application