The Service Principal solution, through the SDK, would allow us to use a Web Job or a Site Extension to perform (automatic or prompted) updates that included configuration changes. However, it would require "too many" privileges - why would a customer trust an application that can, at will, create new resources or update existing ones to increase his Azure bill?
The decision was made to utilize Powershell only for updates - if the customer can see the scripts and authenticate himself, this is not a concern. Sadly, this increases update complexity, but we found it to be a necessary evil.
I hope the above information will be useful for you.