You can just stop the PLME part of your app. The Brown part of app stands independently, and you can get accepted there and not accepted to PLME which frequently happens. Just continue with the Brown portion of the process and drop the PLME. You should let your teacher who wrote the rec know that you are not going to continue with the PLME and it is entirely appropriate to give him a nice basket for his troubles and a kind note.
If I remember correctly, Brown will look at your app independent of your PLME situation. As I said, I know many kids accepted to Brown, very few to PLME when they applied to both. You do have to get accepted to Brown in order to get into PLME, the reverse is not so. You can just send PLME a postoffice card letting them know that you are not applying to that program. That is all you have to do. If an integral part of your Brown app was referring to the PLME program, you may want to call the adcoms there and ask what the best thing is to do. A letter explaining your change in mind might be in order. If little mention was made, then you don't have to do a thing. You are not the first who has done this.
the third rec is specific to math/science, but if you're still applying for an A.B. in, say, biology, then it can't hurt to have the extra rec. in fact, if you're still applying for an sc.b., just not PLME, then the third rec is still mandatory. what program / major are you applying as?