The gap fillers only play a role during lift-off and have no role during reentry. The hypersonic shocklayer over the Orbiter's belly is mostly laminar. However if the gap filler is protruding into the flow then it can cause the flow to transition from laminar to fully turbulent. The convective heat flux from fully turbulent flow is significantly greater than laminar flow. NASA is being super conservative in pulling out these protruding gap fillers. My own gut feeling is the risk to the astronaut performing the EVA is probably greater than the risk introduced by the protruding gap fillers. However it's probably a good exercise to do the EVA as practice for the time when a leading edge RCC tile has popped off and the astronauts must attempt a repair.

Gary