Thank you for your suggestion.
Sitefinity 4.0 will eliminate the need to have web.config entries. These configurations will be kept in separate xml files but will be manageable through the user interface.
We haven't tried this yet, but .NET4.0 supports (the betas) web.config transformations. You might want to try this approach, so the web.config is automatically transformed (sections properties and attributes manipulations) when you build the web site with debug (dev server) and release (production).
I hope this helps.
the Telerik team