Fediverse

I think one of the major tropes present in the show was to demonstrate how there aren't simply white hats vs. black hats (to use cowboy terms). Mal is a criminal, "forced" into living that way bc the government won't "allow" him to live legitimately (except... really? Why won't they again?). Therefore, the presence of great darkness within his lightness, or as you might prefer the presence of occasional boughts of lightness within his darkness, is not a "bug", it's a "feature" of the show, to walk out that yin and yang in a fantasy space opera setting.

Nobody is perfect. Some are far less so than others. Those at least tend to be aware of their imperfections, as opposed to e.g. The Galactic Empire muwhahaha, ahem cough, anyways they seem so stolid, so absolutely certain of their moral righteousness, that unlike the criminal Mal who often isn't such a bad guy once you get to know him, commits atrocities the likes of which would turn people's stomachs, if they knew (hence those are kept as closely guarded secrets).

So I think you missed that: from the perspective of the show, that was no accident - that was literally the entire point of what they were attempting to convey. Mal was not a "good guy". He just had light in his darkness, the same way that the empire has darkness in its light (or is it rather the other way around?).