I see all the speculation about SP having taken tools with them to use to kill MB, in lieu of a gun, and mention that LE is still looking for tools like that, and I feel like it's a case of not seeing the forest for the trees.
Why did SP have those tools? It was to break in, and to use to access areas that he anticipated might be locked and in need of a hammer, a crowbar, and so on. So logically that's what he happened to be carrying when he encountered MB entering the building, and at the moment of interaction decided (or felt forced) to kill for some reason, rather than simply flee. You bring the tools you need for the reason you are there, and the reason the perp had hammer and crowbar and so on rather than a gun was because his tools were break-in tools, not murder tools.
That hints at "wrong place wrong time" murder, and other things fit too.
The deliberate wandering in the building? Looking for things of value. He thought he had plenty of time. He didn't even know she would be there. He expected to be alone for several more hours. The feeling the walls? It was dark and he was somewhat feeling his way the first time down a hall. Why would he think a church had something of value to steal? The better question is, if they did or didn't, how would he know otherwise. He would only have to THINK they had retained a hefty offering there somewhere (and for all we know, maybe they did) in order to motivate him to break into this very secluded large church in the middle of nowhere on the night after Sunday services.
I've never quite bought the targeted idea because it assumes that someone is motivated to murder over a connection so slight and so unobvious that LE can't even find it. If this was targeted, it was someone who went to great lengths to do so, which infers very strong motivation, not just some aggravation. Sure, it's possible someone can murder for the tiniest of reasons, but that's not a likely occurrence. This was not a video game where someone crosses you so the easy answer is to kill them - people don't jump to murder that easily in real life.
Why did he leave without taking anything? Because his search for value was abruptly interrupted, and the risk of staying and looking further (with a dead body on the ground) was suddenly way too high. And if one person (MB) had come, then maybe more were to follow. Gotta go, and save the robbery for a different place instead.