"Why would they give any clue at all?" Assuming "they" - the engineers on 223 - were the ones that gave the star-map "clues", or, indeed, "warnings", again, that's an assumption. But let's say they were responsible, and for a time things were good - the engineers gave man knowledge, fire, etc - but "God" found out, so they started creating bio-weapons to counter God's wrath - "to protect themselves from what?" A being pointing to an arbitrary cluster of stars by itself doesn't impart much information, the point is that the supposition that they "changed their minds" is Shaw's interpretation, I submit that they were culturing life over several worlds to test their weapons on with no foresight or care about humans at all.