One interpretation is that there is a general want for GUND-ARM (Gundam) technology to not be used for war, Given that the "true" Gundams left are the only 4 that were disintegrated, Suletta+Ericht used their ability to exert influence over whatever particle magic system was powering the Permet stuff to achieve the desired outcome.

But yea, for a science fiction "magic is indistinguishable from advanced science" perspective, the finale did feel very magical rather than grounded in science fiction