It kinda does make those paths more moral, actually, assuming those paths don't substitute war crimes for murder (which would be required for any fates worse than death you might bring up). Killing based on your own personal moral code is banned from every worthwhile society for damn good reason: you fundamentally cannot trust a random person off the street to accurately be judge, jury, and executioner.
No matter what their power is, or what they claim their power is, or who the victims are, or whether the existing justice system has failed to appropriately mete out justice, to accept that even one person has a right to choose to kill people under their own authority is to say that anybody can earn that right, and even if you accept the base premise that Atropos is justified in killing these people, nobody can possibly be as precise or as accurate as Atropos has been so far.
As it stands, people are going to try and copy Atropos; not in Brockton Bay, surely, not while she lives and can stop it, but in other cities that she doesn't care about, people are gonna say that yeah, Atropos made it work, surely so can I. And they will inevitably do something wrong.
In the best-case scenario, their inevitable mistake won't be something irreversible, but nobody's that lucky all the time. They'll get a bunch of other people killed as collateral, or they'll kill someone who didn't actually need to be killed, and it will demonstrate that bypassing an existing justice system to kill without oversight is a fundamentally wrong moral position because nobody can be sure that they can kill only people who deserve it, all the time, every time.
Even Atropos herself can't be trusted to do that, because Path to Ending may be infallible but Taylor isn't, and her power presumably won't stop her if she asks it for a Path to end someone who doesn't actually warrant that strong of a response. And if she decides that something warrants death that really doesn't... how, exactly, can you stop her from enforcing that?
Besides, as we understand it, most fair self-defense laws operate under the principle that even in defense of self or others, there is such a thing as disproportionate action. Usually there's a sort of sliding scale, where the less certain you are that the circumstances and resources you have access to would allow you to defend yourself/others without killing, the more lenience you have if you do kill in those circumstances.
But the key there is that it comes down to capability: if you're found to have had, and known about having, a reasonable ability to defend yourself/others non-lethally without putting yourself/others at undue risk, you're still on the hook if you kill them anyway. You can't or at least shouldn't get away with shooting someone in the heart if they clearly intend to hurt you but are also clearly unarmed, too far away to hit you immediately, and you're close enough to your car that you can easily get in and drive away.
And when it comes to capability to end situations non-lethally, Atropos is or at least ought to be very competent at it, given our understanding of how her power works. She clearly has the ability to give her power certain parameters to fill: if she can say "give me the most dramatic and ironic Path to Ending possible", she can also say "give me a Path to Ending that doesn't kill anyone". And we know for a fact that at least in hand-to-hand, she has the option to pull her punches even if her power gives her a lethal path, so it seems pretty reasonable to assume that her power would probably let her get away with ending the gang leaders' influence without ending their lives.
And if it turns out that her power won't actually allow that for some reason, at least she'll have made the effort to plan a non-lethal takedown before jumping right to killing people. Instead, she jumped right from "warning people to back off" to "killing them if they don't heed the warning" without even looking into any intermediate steps along the way. Path to Ending has the same problem as Path to Victory, in other words: if the user doesn't think to ask for a non-lethal option, they're not gonna get one.
Not to mention, Atropos's strategy can only work for so long: she can only keep this up until she dies of old age, then everything will collapse again like a house of cards. And actually, Atropos dying and everyone else having to pick up the pieces is the preferable scenario. If she instead uses Path to Ending to find a way to end her own mortality somehow? I can think of no better situation to create an unstoppable, unkillable, immortal dictator. Big Sister is watching, and she can kill you for things you haven't even done yet, and you can't even try to plan a way to get rid of her because she will know and end you.
Basically, it's less about the details of these specific deaths and more about the fact that considering Atropos in the right for executing these people is an unacceptable moral precedent. You cannot fix an unacceptable situation (which I will concede, Brockton Bay the way canon showed it is also an unacceptable precedent) by doing something else unacceptable: that just leads to a status quo that is differently bad rather than actually making a better society.
As much as I dislike the PRT and Protectorate for entirely unrelated reasons, they're right to want to stop Atropos, even if they're also right to conclude that they can't actually win this fight without better information and that it's not worth breaking themselves to try.