Fix issue where not all pkgs_to_not_remove are checked.

I found a bug in replace.py, where only one entry in pkgs_to_not_remove is performing the "messy" counterpart checks when not in the same SRPM. Essentially pkgs_to_not_remove being altered while looping, and so ending the loop prematurely.

Steps to reproduce:

    yum install php php-pecl-memcache
    yum replace php --replace-with=php54

Expecting to see:

    Installing:
      php54-pecl-memcache
    Removing:
      php-pecl-memcache

Actual result:

    Removing for dependencies:
      php-pecl-memcache

I've included a fix which corrects this issue.