Did the movie even establish that Khan knew where he was going? For all we Know the mobile unit was hardwired to a single location and Khan either did know or didn't know where he was going to end up.
But either way, it was better to use it than crash and burn in his fighter craft.
It doesn't appear that Quonos was a very desirable place for him to be.
But putting him there fits Marcus' plan perfectly.
So he set up Khan to get his hands on it and just wait for him to make his inevitable escape.