I didn't keep up with the news, so I must have missed that leak, because it's the first I've heard of it. But you're saying that the original plot/ending would have involved dark energy, and the reapers destroying sentient life to save them from the horrors of the universe being destroyed by it?

That certainly makes more sense than killing organics to prevent the possibility of future synthetics maybe killing them, but it is still inconsistent with the rest of the trilogy. The Reapers aren't just killing the current organics to save them from an even more arduous fate. They've been doing this for the past tens of thousands of years, over and over again. That means they can't be motivated by the desire to save people, since the universe's continued existence is proof that there was nothing to save those races from. Or is it something along the lines of mass effect drives speeding up the destruction, so Reapers can't allow civilization to get past a certain point of development or something? In which case it's still pretty illogical of them, they don't even try making contact or warning the organics, simply decide that wiping them out is the only way. Not to mention that the mass relays they created and left behind are a huge part of the reason why civilization has advanced to the point it has, so they could have solved the problem by simply destroying the relays.