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Agree with "cut the Gordian knot" answers recommending you change your lead-in to the quote so you don't have to change the quote. The problem with that solution is that you can't always do it. So we're back to your original question. If this is a scholarly essay/paper for a class/journal, then AFAIK you should use , regardless of how ugly or ...
In this example, just move the word in question outside the quotation marks: It is possible for God to desire "all people to be saved." It's more difficult in the case that the word in question is buried in the quote. In that case, you would probably just put the entire word itself in brackets.
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