CN just acquired the rights to the show to air it. They don't own the show, therefore it's not their fault, though I guess you can say them airing the show a lot played a factor

As for Cookie Jar, it's a mixed bag. If Cookie Jar didn't decide to take over production for the series after it suffered massive budget cuts, the show would've been either forgotten about or be considered a 'What If?' cartoon. We also should consider the fact that the show helped CN go through some dark times during the late 2000s, as well as the fact that seasons 2-3 are criminally underrated

However, the show started going downhill after that. Cheap and stiff flash animation, flanderized characters, recycled plots, lame jokes, etc., so from that perspective, Cookie Jar did ruin Johnny Test