The unwanted side effects of simple folder delete or installing over existing installation have been removed by a script written by Kyle Fuller - deintegrate and here is the proper workflow:
Install clean:
$ sudo gem install cocoapods-clean
Run deintegrate in the folder of the project:
$ pod deintegrate
Clean (this tool is no longer available):
$ pod clean
Modify your podfile (delete the lines with the pods you don't want to use anymore) and run:
$ pod install
Done.