Does your roof rack have a center piece that extends the width of the car ?
As long as there is no ceter piece to trip the airflow, I wouldn't think the roof racks would hurt the aero all that much.
I would think the main factor that would hurt the aero in your case ( if indeed tha racks did not have the center braces ) would be the added frontal area.
Then again, you might want to fill in the gaps between those posts to reduce turbulence.
I would think that you could fill in those gaps in the roof racks and actually have them act as an aerodynamic aid, such as the roof vanes that you see on NASCAR and Bonneville racers.
As far as the spoiler idea, I wonder what effect that adding an extention mounted on the roof racks would have. It could catch the air and deflect it downwards, thereby reducing the size of your wake.
Actually, considering the boudary layer airflow and all, this might actually work . Not only would it deflect the airflow downwards, but it would add more velocity to the airstream since it is essentially a sort of scoop that you have added to the top of the car.
The dowside is that that it would add frontal area.
I've got a roof rack with the cross bars and that notion has crossed my mind. The cross bars are certainly unimpressive looking aerodynamically, but short of removing them completely, this seems like a compromise worth trying. I think the change in frontal area would be more than compensated for in wake reduction.