I would like to point out that while the Geth are friendly the Quarians most certainly aren't and it is most likely the organics fault that synthetics wipe things out and in my mind it would always be pre-emptive self defence that is completely justifiable. Robots are reasonable at all times as the Geth proved while organics not so much as proved by the Quarians(they didn't even try negotiating they just assumed the Geth would hate them).
Another thing was is that it never explained what the catalyst was and the Protheans could have very well figured out how to interfere with the catalysts systems and that it was the catalyst alone that could activate the citadel.
I also believe that the reapers and the catalyst did have organic civilisations best interests at heart but in the warped sense that people tend to get when they are removed from the physical world where they assume that their values are more important than others because they are superior. I'm drawing this from the conversation on Virmire when seen with hindsight, mainly the "salvation through destruction" and "we are beyond your comprehension". In my mind this would cause the catalyst to value the way that species flourish when they get to the galactic stage without interference and they probably leave the mass relays because it only values their civilisation at the apex of its glory.
Edit: when you think about it if i was given the choice between letting humanity continue for a another couple hundred years before being destroyed entirely or storing the essence of what we are as a species in a giant metal squid thing to live on for all eternity I'd choose the squid thing that way humanity could never die.
Another thing was is that it never explained what the catalyst was and the Protheans could have very well figured out how to interfere with the catalysts systems and that it was the catalyst alone that could activate the citadel.
I also believe that the reapers and the catalyst did have organic civilisations best interests at heart but in the warped sense that people tend to get when they are removed from the physical world where they assume that their values are more important than others because they are superior. I'm drawing this from the conversation on Virmire when seen with hindsight, mainly the "salvation through destruction" and "we are beyond your comprehension". In my mind this would cause the catalyst to value the way that species flourish when they get to the galactic stage without interference and they probably leave the mass relays because it only values their civilisation at the apex of its glory.
Edit: when you think about it if i was given the choice between letting humanity continue for a another couple hundred years before being destroyed entirely or storing the essence of what we are as a species in a giant metal squid thing to live on for all eternity I'd choose the squid thing that way humanity could never die.