A bit of searching brought this up; Article 5 is especially pertinent:
https://www.newadvent.org/summa/2094.htm
Thomas asserts God's absolute sovereignty over life and death, saying:
"All men alike, both guilty and innocent, die the death of nature: which death of nature is inflicted by the power of God on account of original sin, according to 1 Samuel 2:6: "The Lord killeth and maketh alive." Consequently, by the command of God, death can be inflicted on any man, guilty or innocent, without any injustice whatever."
All the objections and replies are worth a read, though.
While searching I also read the suggestion that the commands we see to put all the Canaanites to the sword was a Hebrew idiomatic hyperbole; indeed we see examples of hyperbole throughout Scripture ("If your eye causes you to sin,..." etc.).
If this is the case, then, as you suggested earlier, perhaps we are not to take it absolutely literally, in which case the moral or spiritual meaning becomes primary in governing our understanding of such passages.
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