So is the reason that 'in' doesn't change the article for 'Kirche' to the dative 'der' here because there is 'movement from one place to another' (per https://www.duolingo.com/skill/de/Dative-Prepositions) ?
Yes. You would ask "Wohin?" ("Where to?"), thus you need the fourth case => in die Kirche. If you asked "Wo?" ("Where?), e.g. "Wo sind wir?" (without a movement), it would be the third case ( => in der Kirche)