They kill. A culture and civilization don't just exist based on the living beings in any one moment, but the progression and growth of all the generations that are and will be born. The thing that was most important, the civilization and the people, are gone. Sure the memories of the individuals might continue, but there is no growth.
It's funny Bioware went this route when both they had Legion and Mordin directly tell the player that a civilization, a culture is based on growth, based on creativity, artistic expression, all the things that are lost when the Reapers harvest. Sure you might still be "alive" but you are no more alive than you would be if you were in a coma that you could never wake from.
Of course the vast amount of constant destruction, horror, and death that is caused by the Reapers "harvesting" all but negates their purpose either in preserving the galaxy for life to flourish (especially since this cycle actually took great pains to preserve fledgling worlds by essentially following Star Trek's Prime Directive), and there is direct evidence that organics and inorganics can get along, but there is no reason to suppose that inorganics would ever want to rule the galaxy since inorganic life would very quickly run out of any reason for continuing to exist owing to how much faster inorganics can process information and come to conclusions. An inorganic in 10 years would have been able to answer the big question of what the purpose of life is, at which point they'd no longer see any reason to continue living. In fact EDI herself suggests this is the case when she and Legion are talking, and he asks her how she can live with humans and she replies "some seconds are harder than others".
And not harvesting some species now so that you can harvest them in 50,000 years is like a death row inmate getting a 5 day extension on his death sentence. He's thankful for the extra time but at the end of the day he'd prefer not getting executed.
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