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Its never suggested that Kirei has such a power. The Church as a whole (remember Kirei wasn't even the church's priest at the time) offered to take in the orphans, and Kirei used that to his advantage. If a large group of orphans went to a church and were never heard about again, most people would be happy. The first thing that would come to mind isn't that something bad happened to them.
The Church and the Magic Association using memory tricks isn't that far-fetched though. And since Kirei has experience with both organizations, its not altogether unlikely that he could manage such a thing.
Memory tricks definitely wouldn't work on Zouken though. Honestly the abnormality in his behaviour is that he participated in Heaven's Feel, not that he skipped out on Fate and UBW.
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