Earlier in the week (link) we discussed why safeik nefashos l’hakeil. Rashi writes that this din is based on the pasuk, “v’hitzilu ha’eidah.” Tosfos (Baba Basra 51b) asks why you need a pasuk – simple logic dictates safeik nefashos l’hakeil, as executing a defendant where there is doubt as to his guilt places the court in a situation of potentially murdering an innocent person.
R’ Elchanan Wasserman explains that basing the din on a pasuk may make a big difference. According to Tosfos reasoning, the defendant who gets off is never really cleared – we just can’t do anything about it. According to Rashi, however, the Torah decrees that in cases of doubt the defendant is presumed completely innocent. There is no longer a safeik – he is definitely not guilty.
A potential nafka minah between the views would be in a case of safeik nefashos by a shor niskal. According to Tosfos model, since safeik nefashos leaves a doubt, i.e. there is still potential guilt, there is little reason not to kill the shor. At worst, there is a loss of money. According to Rashi, however, we grant the defendent, be it a person or a shor, the presumption of innocence so long as there is any doubt of guilt.