The first, and more graceful, alternative is to carefully prep your good references inside your former employer. Relate the short version of what you told me and ask them, as part of their response, to tell prospective employers that while you were, in fact, an excellent employee, a few backstabbers decided to take aim at you. You never responded in kind, but the backstabbing ended up hurting your reputation among those who didn't know you personally. (Use words to that effect -- you don't want different references to sound scripted.)
Assuming a prospective employer contacts your references first and their contacts second, this pre-emptive strike should help. It's uncertain, though, because in a surprising number of cases, prospective employers don't interview the references provided at all.
(Truth in packaging department: Nick Corcodilos covered a similar situation recently and recommended this as the best approach available under the circumstances.)
That leaves alternative No. 2: Deliver the message yourself. This is a tough one. The unwritten rules of interviewing etiquette state that you never say anything at all negative about a former employer or your experience there. (Stray thought: "I see here that you used to work for the Russian Mafia. What was the toughest decision you had to make while you were there?" Answer: "Tough decision? Not at all ... everything that happened there was wonderful, and they'll shoot anyone who says differently.")
Back to business: Somewhere in your future interviews, you explain that the reason you left your former employer was that somehow or other you ran afoul of a couple of office politicians who badly damaged your reputation in the company. As a result, if they inquire with someone who didn't work with you personally, they might hear unfortunate perspectives about you and your work.
If you decide to take this route, you should probably acknowledge that this isn't what you're supposed to say in an interview; it could even damage your chances of getting the job more than the risk that the next hiring manager might decide to talk to other people in the company. I don't recommend it unless alternative No. 1 isn't available.
This story, "When good job references go bad -- and how to fight them," was originally published at InfoWorld.com. Read more of Bob Lewis's Advice Line blog on InfoWorld.com. For the latest business technology news, follow InfoWorld.com on Twitter.