There was a freedom here in St. Margaret’s. A freedom that was part of the air that rustled between the leaves and whispered of an everlasting faith in the Lord, who is the savior of us all. The sexton felt at peace here. A soft wave of tenderness waved over him as he tended the grounds, kneeling by a dry stone wall, ripping weeds away from a gravestone.
The introduction of the sexton is a bit abrupt. Is he only referred to as the sexton? Not everybody out there knows what a sexton is, btw.
A "soft wave of tenderness" is a bit redundant.
The sexton was lonely in a hundred ways; he yearned for friendship or a kindly face to eat his meal with each every night, but his only acquaintances were the tombstones that scattered the church yard.
So, seemingly, he loves the church and its grounds. Yet he is lonely? Usually people drawn to such things are loaners. Is the sexton a main character? If so, you might want to either omit the lonely part, or come up with a reason for his condition.
The setting sun cast a strange coloured light on the floor as it reflected off the stain glass windows. (yet we were just outside pulling weeds?) A tall, graceful man appeared at his place of work, he took an instant dislike to him.
Way too many pronouns. Who is who in that last sentence? Also, "his place of work"? It makes it sound like they moved someplace else, or the guy literally just materialized out of thin air. Try to lead that in a bit more, he hears a sound and looks up from tending the weeds... sees a man approaching through the gates of the graveyard, or something along those lines. And yes, pulling the bucket out like it had been hidden is weird.
Good stuff though. It grabs your interest quickly. Think it through a bit more and let the words flow out describing the scene. Then make sure it makes sense.