Don't take my word for it, please see Post #98.
Natural Selection *should* favor those without the unused code...
Natural selection does not favor those without unused code. Natural selection favors the survival of the fittest. If the G. intestinalis with unused code is the fittest in its ecological niche, natural selection favors its survival. If a G. intestinalis emerged without unused code, natural selection probably wouldn't much care, at least in the short term. It would almost certainly be a neutral trait for survival/procreation.
In the long term it's an open question which one would be favored, because it depends on which one could more effectively adapt to whatever competitive pressures might then arise. If the absence of unused code made the G. intestinalis less capable of adapting, those versions would not be favored by natural selection (if adaptation were required). If the presence of unused code made those other G. intestinalis less capable of surviving, then they would not be favored (if resources were sufficiently limited). And so on.
But your basic statement is simply false. In the absence of competitive pressure, natural selection is merely survival of the adequate...
Don't take my word for it, please see Post #98.