I've definitely had it happen a bit. It usually only happens in a certain situations; depending on what you shoot, you might never encounter it. Moving your eye in the finder can help sometimes, as can rotating the camera by 90 degrees.
Would it deter me from buying an M6? No. Would I get the finder upgrade installed on a favorite camera if it went to DAG for some other reason? Yes.
As it is, my M7 has the upgraded finder and I do find it better. However, the 0.58x finder makes much larger impact on my day to day use than the flare fix.