This is what I would do..
Yes you can take your muffler off and put the stock one, that can help. I would bring the papers that show you passed the emmissions test to the judge if you personally go to the courthouse. Whatever you do, plead not guilty..
Another option which is what I do Is call a Lawyer and they will have it rescheduled (meaning in most cases you won't have to go to court) and rescheduled again until it's dropped.. then they will call it deffered Judification , which will not be on your record at all for a cost of 75.00.
Ive done this 3 times and my record is clean, so good luck..