Honestly, for me the best solution to this problem would be simply increasing unit maintenance (and maybe cost) leading to smaller armies (also, slightly decreasing barb spawn to recompensate for this). Cities alone in civ6 are much easier to capture than those from civ5 anyway, where you needed many units just to take down nightmarishly fortified cities, not to mention units - this time warfare is much less about avoiding city fire.
LESS UNITS FOR ALL CIVS! Less traffic jams everywhere, less AI problems, more individual importance of units!
It would even be more realistic in a way - it feels absurd how pre-medieval armies can fight via frontlines across entire countries, armies in history were small in comparision to the terrain and overall population, until industrial era population boom and warfare evolution leading to long frontlines. That's the interesting difference between 1UPT and SoD btw - first one better models late era warfare with frontlines and country-sized operations, second one better models early-mid warfare with few decisive battles.
As for the enabling religious units to stack with other types - it'd be good change by the way, but a) I am not sure if engine allows it b) The problem of logistical nightmare is of bigger scope than just religious units.