The kashia on 6b develops because the gemara wants to use the kula of beig mitztareif 2 individual eidim in a capital case based on using it lekulah in a mamonos case. Except that the posuk and the logic indicate only that that use of 2 individual witnesses is to obligate someone to pay, not to exonerate him from payment. The posuk says that on the basis of one eid "lo yumat" -- he will not be found guilty and liable to death: the logical conclusion is "lo yumat aval yeshalem" -- in a capital case he can't be held to the punishment but in mamonos, he can.
If the posuk comes to teach us the use of 2 single witnesses is to implicate how can the gemara presume that this goes against the idea that 2 are not mitztaeif to exonerate? Even if you want to say that the gemara (from bamidbar 35:25) wants to find a way to save, not execute, it can't rely on a proof from a case which finds the defendant liable.
Dan Rosen, Teaneck, NJ
We could answer your question by saying that the Torah relies on Eidus Meyuchedes for all monetary matters, and we can learn from a case where the Eidim testify to exonerate someone from payment. However the Rishonim explain this Gemara differently.
Rashi (DH b'Dinei Nefashos) learns that the Limud is that if we have found that the Torah relies on Eidus Meyuchedes for any type of Eidus, then we see that it has a Toras Tziruf, even though this Tziruf is invalid to convict a person of a capital crime. Since there is a Tziruf we may invalidate the Eidus with the rule of Nimtza Echad me'Hem Karov O Pasul. This Limud still relies on v'Hitzilu ha'Eidah, since without this we would say that there is no Tziruf for Dinei Nefashos even l'Kula.
The Ramban offers an alternative explanation. The same way we learn from the Derashah Yumas that Eidus Meyuchedes is only excluded for capital cases and not for monetary matters, we may learn Yumas Eidus Meyuchedes is only excluded from convicting someone of a capital crime and not from exonerating him from a capital crime.
Rabeinu Chananel seems to have a third explanation. He learns that the exclusion of Eidus Meyuchedes from capital crimes is not because the Torah wanted to invalidate such Eidus, but rather because the Torah had pity on the accused. As such it stands to reason that the exclusion is only as far as it leads to exempting the accused from conviction.
Dov Freedman