R. E. Hickock planned the raid on the Clutter home based on info given to him by fellow inmate Floyd Wells. It's been a while since I read the book but I believe Wells, who once worked for the Clutters, told the perpetrators, in effect, that Mrs Bonnie Clutter had mental issues. Now, what if Hickock and Smith had planned to make it appear that she was the perpetrator, by taking her away and burying her secretly in some remote place.
Had Mrs. Clutter been absent when the murders were discovered, might that, coupled with her known mental issues, have misled authorities to make her the prime suspect, enabling Hickock and Smith to get away for good? No doubt, had she been missing, they'd search for her, perhaps a long time, had she never been found.
But I suppose Wells, after hearing of the murders, would still implicate the real perpetrators, as he did in the OTL.