So long as you don't disrupt or damage the supercedure cell, I'd thing removing the queen now would be fine. You may see a gap in brood depending on age of the cell, and from the mating time for before the virgin lays, but the overall colony health should recover quickly from the vigor of the new queen. This said, I'd keep the old queen in a nuc somewhere safe in case you need her back due to a failure of the new queen (birdfood, etc).