[@Shard] It wasn't necessarily the church that covered up the incident, it was his master, who would've wanted to cover it up because Sage was a known associate of his, and if any sort of investigation reached him and uncovered the true nature of their relationship, he would be finished, plus he may had developed some sort of emotional attachment to Sage, kind of seeing him as an adopted son of sorts.  Also though Sage hates the church, he doesn't hate his former master because he doesn't see him as truly a part of the church, just someone who wants to take advantage of it to gain power.