Though I've had some real fun discussions with hardcore pro-destroyers because I disagree with the choices as a whole, I believe they are following the major tenet of the game-the intent rather than the implementation is on their side, IMO.
Destroy was always the goal. Anyone that wanted anything else was either irrational or indoctrinated. An unvarnished true destroy was the only choice that everyone who was of sound mind, wanted and all that Shepard was given "permission" and even was ordered to achieve. It was the understood (though wrongly so) purpose of the crucible. They were all building a weapon to destroy the reapers, not something to alter them or to make them into trained elephants-destroy, that's what weapons do.
The other part of destroy itself is that your love of it can be solidified if you don't care about EDI or the geth-or if you do believe they would agree to die for this. I find this an erroneous way of thinking, but that works for many people.
The other side of it is the ridiculous natures of control and synthesis. Synthesis is poorly explained-what it does, how that happens. All organic DNA is fully integrated with some tech from somewhere. And all synthetics gain full understanding of organics (that no longer exist) and that understanding comes from where? Who knows?
Control is exactly what TIM just died asserting was possible. He believed he could achieve it but was indoctrinated. And then, what does it mean if you can control the reapers. Shepard's consciousness (not emotions, not conscience) will be uploaded into the same infrastructure that houses the kid's program. It's like putting a new CPU into a broken computer from 1990. And, nothing says the kid is gone. Shepard enters the same flawed thing that housed the kid. And Shepard is supposed to control the reapers to protect the Many? Which Many? If some misbehave, who dies? And real people are not going to want the reapers with people goo in them, and reaper variants running around ALIVE. It's kind of a laughable choice. It's even more so when Shepard, in control, starts talking. The music is ominous. Shepard is not alone in there and some of what is said is ominous. Control is also nothing anyone ever wanted (except for Cerberus and TIM).
Destroy is the only choice that superficially meets certain requirements. If it is true and is what happens, it is what everyone always wanted to do, it is what Shepard wanted to do, it is what Hackett tacitly orders Shepard to do, it is what Anderson (friend and mentor) says is the only choice. It is why the crucible was being made. It is the only choice that says it gets rid of the reapers. It also (if true), puts those poor souls within the reapers at peace and removes this abhorrent abomination from existence. Had this been a choice that people had decided to become one with machines, that might have been a different thing, but those "people" within reapers, didn't want to be there. In strictly humanitarian terms, knowing what has happened, Destroy could be the only thing that frees them.