I wouldn't see absorbing as instantly returning them to that world either. Smith in the Matrix can overwrite and absorb anyone without killing them (he does it to literally the entire human race, and agents commonly do it to any human as well), and not only that, but he can also transfer between worlds by overwriting one.
He does that to Bane, allowing him to freely control someone who isn't even connected to the Matrix in the real world, while still inhabiting the Matrix itself and doing all his actions there.
If he gets any overwriting in, which should be fairly easy because there's a lot of targets and they aren't all quite that great and seem to favor melee, he builds a force to deal with things physically (and overwrite more), in addition to possibly tearing Chaos apart from inside out by taking control of the beings within his world. Unless he has some really odd powers to deal with it, they shouldn't be able to just get rid of Smith's code given it can carry on specifically into the real world in a real human while they're not connected to the Matrix, and is noted as something special to him (other Agents can't do it).
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I have no idea who you are, but I thank you for arousing me. - Beruga
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