I'm not discrediting it. I'm simply pointing out that her actions ERASED entire futures - millions and billions of years of futures - from existence, and this kind of decision has far reaching consequences above and beyond simply stopping Comstock. It is a permanent answer to a temporary problem.
The game never even remotely gives the impression that it understands this. We are meant to believe that Comstock is such a horrible person that it is better to destroy an infinite number of histories to defeat him, and I don't buy it. We've had worse tyrants in real life, and we got better because of it. It's not like the removal of Comstock would remove the social injustices of racism and religion. It's not like infini-killing him is going to make the technology that built Columbia cease to exist (or at the very least, be possible) or remove the possibility of it being used for genocide and slaughter.
All I'm saying is that killing Comstock is one thing. Killing all the futures in which Comstock existed is entirely different.
The problem that is being solved isn't "Comstock is a bad person and shouldn't exist".
There are two problems central to the plot.
1. The personal story of Booker/Comstock.
2. The issue of the universe being contorted into a paradox by inter-dimensional travel.
In regards to the second issue, the only way to close off the inter-dimensional loop that has been caused, Comstock needs to never exist in any Dimension. If he is around in even one events will continue to perpetuate. The goal isn't to choose the "best world" it is to return the universe to it's natural state.
Which ties into the first issue, which is the central issue. Booker/Comstock and salvation. Infinite is a story about what happens to a man who is unable to forgive himself because he can't face the reality of what he did. What he is. At the baptism, Comstock allows the idea that God has forgiven him to consume him. He no longer needs to forgive himself. He concedes responsibility to God and eventually to an ideology that says that the ills of the world are not his fault. They are all from the sodom below.
Booker refuses baptism, but that does not mean that he accepts responsibility. Instead he becomes a Pinkerton, a gambler, a drunk, anything to keep from dealing with his reality. To truly atone, both men both men become one and destroy themselves as an act of penance.
Booker is just as "evil" as Comstock. We learn how Booker slaughtered Native Americans with abandon because there where whispers amongst the soldiers that he was a sympathizer or perhaps part indian himself. In another voxaphone we learn that Booker speaks some Sioux, which also implies that he has native roots. (This also explains why Comstock leans so hard towards xenophobia). Booker is extremely violent. He was a Pinkerton. He gave away his child.
The "hero" Booker that we see through most of the game is a broken man who, when given the chance to rewrite his memories, made himself a nobel man who is charged with saving a princess. But the real "Booker" is always there, under the surface, carving a violent sociopathic path through Columbia.