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Of course they can also kill em all, but that would be way farther in the game.
The whole point behind supremacy - "if it's grabable and has no visible strings attached stop evaluating and grab it already!" so if anyone has no qualms about excavating anything that can be dug out it'd be them.
Look at it this way - it's an EARLY advantage. In that regard it's perfectly normal that harmony is looking into the way to soothe the alien agression towards them and that purity is researching the way to keep them away. It's extension of their ideas - harmony is trying to integrate without troubling the "planet inhabitants" while purity simply wants them out of their way. And since it's an EARLY stage it'd make sense that harmony can not yet reach their "non-intrusive" peace, while purity has got their "experimental repulsors" up and running on explorers and don't much care about what the aliens feel about it.
But one argument I have for this being unnecessary, in the long run, is that you will usually gain the first few levels of each affinity as you play the game, regardless of what your focus is. Many essential technologies carry affinity points with them that are useful to any civ (such as Vertical Farming or some of the Alien technologies).
They should shuffle them like this to begin with.