For the same reason I always ultimately save the Chargers my Inquisitor doesn't sacrifice assets for something unproven or superfluous. For the Chargers ... I don't know what I'm actually getting from an alliance with the Qunari, but I do know exactly what I'm getting with them and she was unwilling to sacrifice tried and true for something unproven and vague.
I don't save the Chargers either.
Yep... I'm a terrible person. I let Blackwall rot and I don't save the Chargers.
What Blackwall did he did out of greed. He knew before hand that what he was doing was for money and status. He heard those children and for whatever self serving reason, be it pride or greed, he killed/allowed them to be killed. Unless his men were deaf and blind, they must have heard/seen them too. Just because a superior officer gives a soldier an order does not mean that soldier should follow orders blindly. Following the orders of a superior is still a choice.
I am also a believer in second chances. If you show up late for work, dull my favorite blade during practice, forget a special training session, maybe got a little rude with a visiting dignitary... sure... I'll give you a second chance. Things like that deserve second chances. Senseless murder is a whole other critter.
The best predictor of future behavior is past behavior.
When Blackwall was a child, he saw other children being cruel to a living being, watched as they tortured it then ran and hid while they killed it. Sounds a lot like, he heard those children crying in the carriage, watched as his men killed them then ran and hid while others took the blame he should have shared. He knew what he was doing was wrong, yet he did it anyway. It doesn't seem to me like he changed much at all. Not only that, but I do believe that could have been considered his second chance... and yet he blew it.
And with the Chargers. I refuse to lose an alliance with an entire nation... one so strong that at one time had "fought all the lands of Thedas to a standstill." The Qunari were only a few hundred strong when they took Kirkwall, and has kept the powerful Tevinter magisters from taking one island for almost one hundred years. They have dreadnoughts to help us patrol the seas, and have developed the explosive gaatlok which, for the moment, is theirs alone. They have a strict code of conduct that insures no deceit or treachery to threaten the Inquisition. I will not sacrifice such an alliance for a handful of men.