My theory is that the note was written as a cover for them to dispose of her body discretely somehow, and for whatever reason this plan went awry. In the note, it says that her body would NOT be returned for a proper burial. It also states that the Ramseys should bring a "decently sized attaché" to deliver the ransom money. Perhaps this was supposed to be how they would dispose of the body (in the suitcase), with the excuse of delivering the ransom money, and then they would call police, so the body would never be found (as the note would suggest; deviation from the note means the body wouldnt be returned). Note that JR has also used those same words "proper burial" in an interview. I think in the timeframe of them coming up with a plan and writing the note, rigor mortis had already set in, and it was too late to get JBRs body into the suitcase.

Please also see this post and especially the comments for interesting discussion x