Rebbi Yehudah is simply saying that since the possibility exists that there is a conspiracy here, we should not kill more than one pair of witnesses who become Eidim Zomimim in any single case. Otherwise, one can have the possibility of people being Mazim anyone who is Mazim their friend, and the killing will continue. Rebbi Yehudah would rather err on the side of caution and not keep killing people due to this possibility. (This is a simplification, but should be enough to answer your question. For more in depth discussion of this matter, see the Tosfos Yom Tov on the Mishnah.)

All the best,

Yaakov Montrose