Your logic suggests that the life of the body is more valuable than the life of the soul. If those babies were innocent of sin, their souls were saved in that moment. Had they been left to grow up in that culture, their souls may have been corrupted. Either way, the physical body is dispensable to God because we are not our bodies, we are the souls contained within.

If God's goal, is to grow the souls on earth to be worthy of heaven, rather than spoil the human being on earth, then making corrective moves here and there on the timeline could be seen as mercy on our souls, and not some kind of injustice against the physical form.