If you accept the player back, you have to pay their ML salary.
If they have MiL options, you can put them back in the MiL, but you still have to pay the ML salary.
If you put a Rule 5 eligible player on your 40-man, you can't lose him. Then you won't ever have to make this decision.
Now that WIS has made it so top prospects are automatically protected, preventing new owners and owners who are away for a few days from losing their best prospects, the Rule 5 draft seems to be a very good equalizer that somewhat narrows the gap between the better owners and the rest.
For most worlds, this seems to be a good thing. Helps keeps worlds more competitive.