So Hydras plan was to kill all dissenters based on their electronic profiles. However, the saying bombing for peace is like fucking for virginity comes to mind. It is a dumb premise. Those guns on the ships weren't exactly low key, so if they initiated, so people who died to them wouldn't exactly just die of cancer or some other way where the people around them wouldn't know what happened. They'd have to do a purge every day when friends and families of the victims start reacting. MARVEL seems to be in the "real" world so to speak, and in our world, if people started being blasted out of the sky by government organizations, other people would be upset.
Further, they can only target one area at a time, even though it is large in scope, if China, Russia or whatever else large military power found out that millions of Americans were being blown away because they dissented to being run by the government or had other ideas that the algorithm deemed dangerous, do you not think they would act long before the three ships would be able to position themselves to take out the dissenters in those countries? The three ships would have to be on the move all the time, just shooting the constant increasing number of dissenters to the point where they wouldn't have ammo left while also defending themselves from missiles being launched by every country capable of launching one.
As an action movie, I enjoyed it, but even the plot in Iron Man 3 with a fake terrorist war being planned is more believable than that as that premise was to create tension and profit for it. HYDRA wanting order, by killing millions across the world, with three ships using conventional ammunition makes you have to completely suspend any sort of realism and go into "well it is a superhero, action movie, realism is out of the window already!!" mode to enjoy it. Making it more into a mindless popcorn movie rather than taking it seriously, which they obviously want you to do considering how much it plays on conspiracy realism on why data collection by governments can be bad.
If HYDRA managed to do it, there wouldn't be order, it would be world chaos. Smart enough to create AIs and infiltrate the top levels of organizations and governments, while still failing psychology 101? Fun movie, but one of the dumbest plots yet.