In «غَيْرَ مُفْسِدِهَا», ghayr excludes the harmful case, while mufsidihā points to the possibility of spoiling or destroying the dwellings. The full expression restricts the kind of rainfall being requested.
The prayer «فَسَقَى دِيَارَكَ» is grammatically intelligible without this qualification. Rhetorically, however, the qualification protects the intended blessing from an inference that would make the prayer harmful. Thus a seemingly minor phrase can be essential to expressing the speaker's true aim.