I am certainly relieved to hear that when the church said "exterminate" it didn't mean "kill" it meant "send somwhere else".
Whew. I wonder how that misunderstanding could have developed.
You brought out this quote as an example of St. Thomas Aquinas using the word "to exterminate" to mean "to kill." If you were right, an equivilent reading of the sentence would be "...to be killed thereby from the world by death." That sentence makes no sense and thus fails to support your assertion.
OTOH, if TA used "to exterminate" to mean "to drive out," the sentence would read "...to be driven out thereby from the world by death." If I'd never heard the word exterminate before, this second interpretation is the one I'd conjecture from the context.