I tend to agree with Big Uncle that this is a teaching story, where two Buddha emanations demonstrate something we are supposed to learn. So, I note that Kundeling Rinpoche had been mixing the Gelug with the Nyingma dharma; the Gelug dharma and the Nyingma dharma are both really excellent, of course, but the point of each is that if we follow whichever one is right for our own karma, we would become a Buddha on either path; mixing it haphazardly without a guru's blessing would be problematic, because while we might think we were practicing a lot, we might turn out to be distracting ourselves from what we really need to do. ( That said, sometimes it's okay, as long as a trusted spiritual guide helps us, like when Nyingmapas used to learn Ganden philosophy at Geshe Kelsang's monestary, while keeping their daily practice Nyingma. Obviously, since they must have made arrangements with the monestary, this was okay with some enlightened Rinpoches. In other words, that arrangement must have worked well for the practioners in question to reach Buddhahood.)
So I agree though, that in reality the Buddhas don't really punish people, though they might do something wrathful to clear the karma of sentient beings, but as it's a teaching story, I guess its supposed to just make clear that it's generally not helpful to mix doctrines.