Symbolism, Imagery, Allegory
The lieutenant aspires to create a place where no memories of the Church remain, but signs of the old religion persist despite his best efforts. What did he expect? To just erase the Church from society's collective memory? That might be a little ambitious, even for us.
No bells ring at noon, as they once did, but on Sundays shops still close at noon, a "relic of the old time" (1.4.77). On his way to the docks, Mr Tench passes by "the Treasury that had once been a church" (1.1.2).
Religious books are banned, but pious mothers still acquire them and read them to their children. The people still believe in God even though many years pass without their seeing a priest.
Both out in the open and behind closed doors, the suppressed Church continues to shape the society that persecutes it. In Greene's reckoning, the Church survives, even under widespread persecution.