Tosefos on 21B asks how could the BYSUSIM send false witnesses to testify that rosh Chodesh is early to make the second day of Pesach coincide with Sunday, wouldn't they be eating Chometz on Pesach? He answers that they agree with the Drasha that althogh Bes Din was duped into making Rosh chodesh on the wrong day, but that is the day and Pesach will be the 15th day of that month. (ATEM AFILU MUTAIM)
The question then arises HOW did the BYSUSIM resort to sending the fire signals on the wrong day to fool all of Klall Yisroel. What purpose does this serve? If they are truly worried about Pesach being on the proper day then Pesach will be on whatever say it was SUPPOSED to be according to the way BAIS DIN sanctified the month NOT according to the way they sent the signals. Therefore it would seem that their sending the signals would do nothing more than "mess up" the rest of Klall yisroel. They however wquld still be forced to keep the 15th day of Nissan the way the Bais din edecalred it by way of their Kiddush Hachodesh.
Excellent point! The RASHASH asks another question: Even if the Baisusim thought they could fool the Chachamim into bringing the Omer on Sunday with false witnesses, how could they fool them with torches? Only the distant people would be fooled with torches, not the Chachamim in charge of bringing the Korbanos, who were in Yerushalayim and heard Beis Din announce the real day on which the first of Nisan occurred!
He answers that the first story specified "Baisusim" hired false witnesses. The Mishnah, later, mentioned that "Kusim" tried to confuse the Jews with the torches. They just wanted to cause as much confusion as possible, not necessarily to get the Omer brought on a Sunday. (The Kusim would do this every month, and not just for Nisan.) This answers your question as well; the Kusim did not believe in the Chachamim's months at all, and just wanted to confuse others. (They had their own system of months, for their own purposes, undoubtedly.)
By the way, Rashi (22a DH v'Im Tzudah) also mentions the two groups of plotters against Kidush ha'Chodesh separately, Baisusim and Kusim.