Is there any openings next to the fan slot you can open to vent the air out? I would not feel too safe blocking the fan out on that card. Even if you only use that single bracket, you would want to have some space for the hot air to exhaust out from the heatsink.
The card will fit if take off the top cover. Since the fan is directly on top of the heat sink I don't see why the cover is needed to vent air. There are plenty of room above the fan to allow heat to be exhausted, I wonder if it will work fine.