I struggle with cases like this because
> oh, well I'm a compassionate being just like Mahakala, therefore I should be able to hit my child because I know what's best for them
DOES seem like a reasonable "emulation" of this supposedly enlightened and perfected figure -- the only way to truly know when you're being compassionate and when you're not is with perfect wisdom, and so long as we're all stuck on earth that's not exactly attainable. As an applied practice, it feels two-faced, and I feel similarly about all "secret" doctrines and figures. Other religious figures, like Gautama Buddha or Jesus or whomever, are much preferable in this way: emulation of them is a strict good in those traditions. You don't need to hide any part of Gautama's life, or save any part of Jesus' teaching until later. Within their traditions, emulating either is essentially straightforwardly positive.
> And we should also put these symbols into the context of a Buddhist worldview -- that a human life is not guaranteed, and even if we get one and survive into adulthood, most will go about their regular lives without using this opportunity to do the deep work necessary to escape our self-inflicted cycle of suffering
But this fails to explain the necessity of such a contradiction -- how can a perfect being be the one to embody such cruelty? To elaborate on what I'm getting at,
> So that's all to say, we should focus on the metaphors that they embody rather than their literal depictions.
But in this case the metaphor is what -- that cruelty, or at least the pitiless annihilation of innocents, is an intrinsic quality of even a perfected, enlightened being? This is a real practice that is actualized in the real world, with (to my understanding) whips and the like being a common feature in the upbringing of the Dalai Lama, with these wrathful deities serving as justification. The symbology and iconography of these deities goes far beyond a "memento mori" -- examples from other cultures show that simple depictions of skeletons or even skulls can capture that. Clearly the wrath is a key part of this depiction, otherwise there would be no risk of "oh, well I'm a compassionate being just like Mahakala, therefore I should be able to hit my child because I know what's best for them".
One who becomes Christ-like would certainly not go around "fighting fire with fire", regardless of what message they were trying to get across, and while I am certainly less studied in Buddhist doctrines I truly struggle to imagine that Gautama Buddha was thinking that other Buddhas would do so either.
I will admit that most of my understanding here specifically comes from Tantric varieties of Buddhism, so it's possible that the depictions and representations I describe above are peculiar to that and don't generalize.