As you know, there were no 'national' laws. 
There were hundreds of tribes of native Americans. Many of the native Americans had on-going brutal wars amongst each other -including horrible forms of torture.
The early Europeans were explorers. Many were friendly to the native population, since that was conducive to their mission, and to trade.
The Church's blessings were with good intent for a safe journey - they were not 'blessings' to go annihilate anyone.