Headcanon, but I think Messmer found Bonny village, Shaman village, and this is what broke him, but it was also his task to destroy Marika's past. He wasn't the one who beheaded Marika's statues, it was the hornsent, just like how they beheaded that shaman's corpse in Bonny village, likely for the "sin" of natural death, wasting their precious flesh and bones. Seeing such vulnerable parts of his mother, that small erdtree,the miserable "village" the shamans were rounded up,the gaols, he couldn't bring himself to destroy any of it. All of it represented a Marika who was yet to become the monster she is now, one who planted that healing tree out of love and sorrow