Whatever approach you take, if you remove from Crm any fields used by the website, then that will stop the website working.
You could create a custom API in between website and Crm, and keep the custom API interface fixed, which may prevent errors in the website, but if you remove fields from Crm, then you just move the problem to between the custom API and Crm.
Overall, it doesn't really make a difference which architecture you use
Microsoft CRM MVP - http://mscrmuk.blogspot.com/ http://www.excitation.co.uk