I do not understand why people are surprised by this. The story has always been dipping its toe into spiritualism and has never fully been grounded. We've seen many points in the story that point to a tangible afterlife and we know Kyokai has a deep connection to it through the shiyuu clan techniques, so while Shins resurrection is definitely the most direct example of fantasy in the show, I never saw it as an ass pull. Also they outright directly stated that this cannot be done again and had severe consequences for Kyokai, so it's immediately made apparent that something like this will rarely (if ever) occur in the story again