Well, there are two possibilities:
a)They wanted to kill her and get rid of the body
b)They wanted to kidnap her and use her.
Now, the first option seems a bit silly, as there must be an easier way to hide a body - throwing it out of an airlock, feeding it to the recycler, dissolve in an acid... or even just cover her up with some scrap.
So the only logical option then is the second one - the rebel Belters wanted to keep her alive and use her, hence why she has been kept in an air-tight container with a life support. So why did the ship didn't dock to collect her?
Simple: they knew that the security has found Monica and put soldiers in her place. Marco Inaros had a mole high in the structure of the Tycho Station working with Fred Johnson himself, who has managed to inform the incoming ship about the trap, so they had to revert to a "plan B" and instead just used a robot to steal a protomolecule.