Kyubey, has seen magical girls do impossible things before, he implied this during his chat with Kyoko, now he has seen it done enough times that he's unable to tell her that theirs no way for a magical girl to turn back a magical girl back from a witch, even though this is a thing he has never seen happen before. How ever when Homura asked if Kyoko could of done it, hes say's of course not, this is simply that before hand he did not posses the information to know if she (Kyoko) could do this impossible thing, so when she failed, he has all the information to say that she had no hope of ever doing it, this is truth because he has no information that it is untruth. After all who says witches were their at the start of the magical girl system? Were we there to see it?