How to re-create content types using the feature module which removes deleted fields?
The answer to your question boils down to what is mentioned by the Features maintainer in this comment, i.e.:


  FInally going to mark this as "won't fix" until somebody proposes something better.
  
  1) Features will never do anything that might cause content to be lost on your site. This includes deleting fields. Just because you remove a field from a feature doesn't mean you might not still have content stored that would be lost if features auto-deleted it. I've never been in favor of any sort of auto-deletion.
  
  2) Now that fields are split into bases and instances, this gets even more complicated.


The next comment in that same issue includes a link to a 32 steps process, which describes Deleting a Drupal Field Saved in Features. IMHO this is "as good as it gets" today (and my recommended work around until further notice).