It would be much more natural to put it at the beginning: "Sometimes I don't go to church". Even then, it sounds a little clunky as a standalone sentence. It works better in a positive sentence - "Sometimes I go to church"/"I go to church sometimes"/I sometimes go to church". To use it in a negative statement, it's OK with a preceding positive statement - "I usually go to church on a Sunday but sometimes I have something else to do so I don't go".
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