Brainstorming what's my main reason not to choose control:
Self preservation. I want to live and simply cannot get myself to 'commit suicide' even if my spirit will live on (in some monstrosity). The urge to live on is even bigger than the grief of sacrificing EDI, LEGION (and the entire geth for that matter). IF... I would have had to sacrifice, say, my LI for the destroy-option however, then I'm not so sure I 'd always pick it!
Also, for the synthesis option, who am I to unilaterally decide that all organics becoming half synthetic and synthetics half organic is good for life. "Big picture made of too many little pictures," to quote one of my favorite friends in ME

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Secondary reason is the thought that tells me: "Reapers WANT all threats to them to either advocate control or even (more or less) synthesis," so it cannot be good. Perhaps this reason is my personal means to justify the end which automatically returns me to:
self preservation.