The short term solution is "references available on request" on the resume. Never let people just randomly contact your references with your knowledge and without your ability to provide context.
The effort to contact a candidate, ask for their reference info, then contact 3 or 4 references and ask sensible questions and take notes can easily exceed an hour or two. In that amount of time I could interview you. So if you seem like a good candidate, I'll probably interview you and then ask for your references if you make it to the "good" pile after the interview. I think I'm pretty representative in this. Recruiters are often rabid about demanding references early and often; this seems to be primarily driven by their desire to use that contact info to find leads more than to vet you.
So, you're in the interview, everything is going great, and the interviewer says "oh, I will need those references if you have them handy." The moment of truth. I would have with me slips of paper with the reference info. Each would say the company, the general contact info for the company, and then one or more people with a role and some contact info specific to that person. I would hand them over with an explanation for each.
Here is for my first job at ABC. I worked for Peter Smith, who has since moved to another company so I've included his updated information.
This allows them to contact ABC for generic "HR records show" kind of reference, and Peter Smith for "I liked this employee" kind of reference.
Here is for my second job. This one's a bit tricky, it was a small startup and Steven Jones, who I worked for, tends to give everyone horrible references as revenge for leaving. I know that's hard to believe, so I've also included two coworkers, Sue Able and John Baker, with their current contact info, so they can confirm that for you. I'm sure you'll want to talk to Steven but I hope you won't give too much weight to what he says.
Not dancing around it, and able to back up your claim.
Here is for my current job. I would prefer if you don't contact them right now, because they don't know I am looking for a new job. Once we agree I'm a good fit here, and you're ready to make me an offer, if you want to make it conditional on a good reference from them, I'm fine with that, but I would like to be the one to tell them my plans.
This is also very common.
Then immediately after the interview (like while you're headed home from it) contact all your references to let them know you have given out their names and to expect to be contacted. As a reference I always appreciate that heads-up.
If someone gave me these I probably wouldn't even contact the alleged nutbar until after I'd talked to the coworkers - if they confirmed the nutbar story I wouldn't call to hear the rant.