You should be able to just remove the Gmail service from your account (after making sure any possibly useful information from it is backed up). If you don't already have alternate email choices, you should be prompted to add one so your account will still have a username once Gmail is deleted.
It's possible that your displayed username for services like Google Code will change (since it seems to use the primary email address if the account in question doesn't use Gmail) but there should be no real problems, only changes in how your profile appears.
Searching through the Google Accounts help documentation, I can't find anything on changing your Primary Address if you use Gmail; it seems to be a choice made for you.
Edit (prompted by Robert Norris): I would very much love such a feature, as I am prevented from logging into my AdSense account using the same username as every other Google service I use. If I could link the two Google Accounts, I would probably stop hating Google for shutting down Notepad and Jaiku (but not for shuttering Gizmo5, even though I already have an account).