Answer

According to the tradition we received, together with the Written Torah, an Oral Torah was also given. The midrashic interpretation does not come to replace the plain meaning, nor does it need to fit it. It is a parallel interpretation. Therefore, the fact that the halakhic conclusions do not always fit the plain meaning of the Torah should not be troubling at all.
Of course, one can ask why the Torah did not simply write the midrashic interpretation directly if that was its intent. Various answers have been given to this, and I tend toward the view that in the end, Jewish law and the halakhic outlook are a combination of the plain meaning and the midrashic interpretation. On this, see the series of three articles by David Henshke in HaMa’ayan 5737. There he also explains in great detail the law of piggul that you asked about.