I think what you're getting confused by is that you think we were supposed to understand Roe2's speech, when we're supposed to be just as confused as Minori. I bet the show will slowly explain everything she said and everything will make sense by the end of the season (hopefully, if not we just have to keep reading the LNs).
Here's my (probably shitty) explanation of what Roe2 meant, she was using big fancy words about how it's best to have a society where the majority of people are happy and let the unhappy ones leave since it's impossible to have a society where everyone is happy that doesn't fall apart (or at least start causing everyone to be unhappy). When Minori said, no, she didn't understand, Roe2 seemed to imply that the reason she didn't understand was that her intelligence was somehow limited by some rule of the physical world.
The bit with the Empathions was Roe2 saying that Minori thinks that her loneliness only affects her, but the sorrow is in fact shared with everyone around her. Now, I'm not sure if 'empathions' are supposed to be some kind of physical particle (it seems to be what Roe2 is implying), or just a way of explaining collective feelings. Building on what I explained above, I believe Roe2 thinks it's a good thing when someone drops out of society, because they take their 'empathions' with them instead of sharing them with others and thus dragging down all of society.
Hope that helps!