Personally I never felt like Destroy was even an option. 

First of all, there's no reason to believe Starchild is lying. If he is, why does he even give you the Destroy option? Why make up a needlessly complicated lie? He could've just been like "Nah, that red thing over there? It's just a trash compactor, don't worry about it." 

The fact that the geth are synthetic really shouldn't factor into it at all imo. Regardless of whatever ambiguity was present in the first two games concerning the sentience of the Geth, by the end of the third game they are undoubtedly sentient beings with just as much a right to life as any other race. I wouldn't kill the entirety of the Human race (though that would've made for a pretty poignant and interesting ending), or the Turians, or the Asari or anyone else, not when there are other options available (which there are). And saying the Geth are a liability because some of them supported the Reapers is like saying the Humans are too dangerous because Cerberus almost fucked up the galaxy too.

Both Control and Synthesis are more viable options, imo.