Yep. It was pretty obvious from the get go. Just as it was obvious Marty was banging that clerk and Tuttle was a villain from the first time you saw them in episode 1. Like the writer says, the show isn't trying to trick you. You're not going to get extra fan points for noticing these thing, it's just playing them out expertly.
This gives me the most reassurance it wont dissapoint. It's not a Broadchurch style "lets make it the least likely person and obfuscate everything to keep suspense" whodunnit. I don't think it's going to throw us a curve ball. There is a conspiracy, it involves the church and a big man with scars on his face, Rust & Marty will get back together to solve it. Lets just see it done well.
Maggie's motivations didn't bother me, only that she dropped Rust in it. It wouldn't have taken much to at least say she threw herself at him. Especially if her purpose is to goad Marty. The way she did it seemed to be wilfully pitting them against each other.
The only other tiny thing that bothered me was the "slow minor key classical piano music in a mental asylum" trope which seemed a bit naff for such a good show musically. Tiny nitpik though, and absolved by the great version of "Sign of the Judgment" at the end.