AYC: Rashi says it because the Pesukim are Meduyak that way. Whether or not it actually happened (Hakadosh Baruch Hu obviously could have made it happen to teach this lesson) the fact remains that rocks (and food) do not have Zechuyos because they do not have actions. They do whatever Hakadosh Baruch Hu created them to do and have no say in the matter.
There is an entirely separate issue in Kabbalistic traditions that sometimes Neshamos come back as inanimate objects because they need a tiny Tikkun and have to be involved in performing some type of Mitzvah. That is still not a Zechus for the inanimate object, but a Tikkun for a Neshama that Hashem decided needs to be involved in something particular before Hashem will judge it.