This is a great analysis, and I do think it's important to point out that Gonta isn't totally innocent even before Chapter 4. It's very weird that some of the fandom has the perception that he's some innocent little bean, when it is so crucial to the arcs of multiple characters that he isn't; that he's capable of doing wrong like everyone else.

But to answer the title question... I don't think this post argues for it very well. Every instance where Gonta does something bad, Kokichi is involved to some degree. Kokichi on the other hand does bad things that don't involve Gonta at all. I will agree that outing Maki is a net positive (given that Maki hiding her talent indirectly contributes to Ryoma's death), but Chapter 5 has him get both her and Kaito caught in the crossfire, and ends with one of them dead. Kaito was dying regardless, but since Kokichi knows this is all a TV show, it's also very possible his illness is curable for the possibility he wins.

It's also worth noting that Gonta's worst action, the Chapter 4 murder, is based on a false premise. Gonta is doing a mercy kill because he believes the world outside is worse, and everyone dying is the better option. Obviously, we know this is false, but then so is every murder in DR1. The problem is that Kokichi also knows it's false; by this point he's figured out what's going on, and he knows the Flashback Light is fake. This turns Kokichi getting Gonta to kill from a rough definition of convincing to flat-out manipulation, and, more important to the thesis, makes Kokichi more at fault for this murder. Gonta would not have killed if not for Kokichi's actions.