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We see Jim Phelps murder his wife, needlessly, and yet, only give Ethan what amounts to a glancing blow.
Why wouldn't he just kill Ethan and try to escape with his wife instead of taking the risk of leaving him alive?
The only valid explanation that comes to mind is that Jim Phelps wanted to frame someone so the file could be closed instead of an open-end investigation that could lead to his capture ultimately!
Jim just wanted to leave as soon as possible after taking the money. He had killed his wife because she was ordering him to not kill Ethan and also because it seemed she was soft/ taking a liking to Ethan.