The Geth dying to the Red Wave is just one more reason the endings are bad in ME3. Geth are SOFTWARE, and a red energy wave SHOULD NOT be able to differentiate between the 100111010 of a Geth and the 0110100101 of an Environmental program inside a Quarian Lifesuite, which we know from talking to Tali if you save both, that the Geth are loading themselves into Quarian Lifesuite to simulate illness to kickstart Quarian immune systems. We where hit over the head that Geth are software, and to make a point and to try and make the ending decision harder, Bioware decided to ignore this and kill them anyway.
To me, after the Geth Fighter Squadron mission, talking to Tali in ME1 about the Morning War, and seeing the unrelenting hatred and attacks on the Geth, my sympathy is with the Geth over the Quarians. At least Tali seems to get it, but most other Quarians are too mired in their hatred and bias for me to feel any remorse if I have to pick between them and the Geth.