Throughout the saga we see Palpatine executing plans buried within plans, as he hides in the shadows. I don't think this is any different.
I think that Vader made the show of nearly killing Marek to plant the seed of Rebellion in him - no doubt Kota would have detected Marek as an utter slave to Vader, and not joined him.
Vader trained him ostensibly to kill Palpatine to deceive him, make him move secretly so the Rebels wouldn't know what Marek was, in my interpretation, so that they would follow him later.
It was then the arrogance of the Sith that let them think Marek was destroyed on Corellia.
That's my perception, anyway.