Do you actually have any reason to think they will give you a bad reference? They are unlikely to do so simply because you are leaving after a few months - if that's the only issue they are likely to give a basic factual reference as Hassled says.
You could choose to leave the employment out altogether, assuming you will have something decent to say about why you have not been at work for x months. I wouldn't advise you to leave it off your cv and then bring it up in an interview though - either leave it off altogether or deal with it.
Sometimes it doesn't work out and there's no shame in admitting that and taking the initiative to move on to something that suits you more. Don't slag off the employer in an interview though, that makes you sound bitter and twisted and will make an interviewer wonder if it was partly your fault. Just explain in a neutral way why the job/company wasn't right for you, and how the experience has helped you clarify what you are looking for in a job/employer, and therefore has helped you identify x,y,z job/employer as somewhere you want to be.
Just to mention also, you may find it very difficult to fool a payroll department into believing that you haven't been working for months, because of tax records and suchlike. Not necessarily a problem depending on what kind/size of organisation you apply to. If it's somewhere huge and fairly anonymous it probably won't matter, but otherwise it might.
My advice would be to deal with the employment properly when it comes to potential new employers and to speak to HR where you are now about the kind of references that are normally given.