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I am not going to debate your points about threesomes being right or wrong; you are certainly entitled to your opinion either way. If opposing it makes you happy, so be it. But i think you are missing the point. The problem is not her past behavior, but his current approach.
If her having a threesome in the past is so bad, why doesn't he leave her? He is totally in the right making her past is a dealbreaker (as it seems to be because of his behavior towards her since) but if he does, he should leave. It is not up to him to punish her for the rest of her life. Cary, you are right, she should leave him, if for no other reason, because he is too weak to do so himself.
Also, remember that by the end of Chasing Amy, Holden realizes that he made a mistake.