There is no secret chamber in the church. The game maps actually contain multiple dungeons or levels (see below), but you are only shown the region you are in. You are probably seeing creatures from a different area. Also, it is possible some areas were changed before release, leaving creatures stranded outside of the play area.
Map (30KB) - showing several dungeons and sewers south of Rivertown, which normally are blacked out when not in each area
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