i'm not sure how much kishi was behind the filler, but the killing a pain part is definitely canon.
putting that into perspective, kakashi was able to kill one pain and almost 2 (albeit the strongest ones)
shizune lost to the human pain
ibiki and others managed to capture the animal path
ebisu or whatever his name is, and other chuunin, lost to the same pain konohamaru fought
those are all jounin or elite jounin, yet konohamaru who is barely a genin was able to beat the albeit weakest pain. he already has kage bunshin and rasengan under his belt, whereas naruto had just kage bunshin at that stage. He also has superior taijutsu and speed to at least naruto in the chuunin exams, probably more than sasuke at the time he fought haku too. Naruto was right when he said that he gets jutsu much faster than naruto does, he will progress insanely quickly. especially if naruto teaches him that kage bunshin training method as well.
note: at this point, konohamaru has just become a genin, ie at the point where naruto and sasuke took their first c-rank mission vs zabuza and haku. he's definitely better than them at this age, although not as good as them post-chuunin exams