Why should this be a problem? We never get any indication that the nebula would for be a barrier for the Genesis wave in any manner. Obviously, it is going to reach Kirk's starship unless Kirk goes to warp - so just as obviously, it's going to reach a planetoid that Kirk only very recently departed at damaged impulse.
Perhaps it wasn't the Genesis Wave that was the threat Kirk was trying so desperately to warp away from. Perhaps it was just that at the painfully slow speed at which they were lumbering away from the Reliant
and with shields non-functional, that the detonation of the ship's matter/antimatter reactors, whether by Genesis or otherwise, would destroy Kirk's ship.