papal armies

is there a way to stop/mod papacy from attacking & taking reb settlements?

Get there first. :yes:

:egypt:

Or, move so as to block the Pope's men or ships. He does get ticked if you move troops into his territory, however.

You could mod the files and make the pope passive.

In descr_strat (data/world/map/campaign/imperial_campaign) you'll see each faction has a title like "trader henry" or whatever, altering those changes the factions behaviour.