The reason the Catalyst is so pissed in low EMS destroy is because it is about to lose the war it's been waging against organic life since its creation. It has no way to physically stop Shepard at that point and no way to persuade Shepard to commit suicide.
"So why did it bring Shepard up to the decision room?" "Shut up. Maybe the elevator was automated or something." -- Mac Walters & Casey Hudson: "More speculation for everyone!"
The only reason to choose something other than Destroy is because you buy into the bullshit the Catalyst is spouting and because you're sentimental. Or because you've been conditioned to jump at the possibility of 'heaven on earth' without thinking through the consequences. Or maybe because you put no value on free will. Or maybe you enjoy the idea of martyrdom. Or maybe you buy into the "Shepard is Jesus and must die for our sins" symbolism the writers have been trying to impose.
Too much Star Trek got dumped into Mass Effect. It started with Mass Effect 2 and its 'humans are special' theme, and the bullshit lines about how the Reapers "absorb the essence of a species." Plus powers like Reave, which blurred the line between the gravitic / inertia altering properties of the mass effect and sheer magical healing.
This was compounded many times over in Mass Effect 3, with both EDI and the Geth being forced through "Pinnochio" story arcs instead of continuing to be explored as alien, if understandable, life forms.
And then there's the frustratingly cringeworthy line about how adding "your organic energy" to the beam would force a change in the DNA of synthetic life. There are SO many things wrong with that statement. "Organic" has a very specific meaning; it means a carbon based compound or carbon based molecule. In a broader sense, it means cellular and multi-cellular organisms with a carbon-based chemical structure.
So what is "organic energy?" Energy, too, has specific definitions. In the context of technology, it is the usable power derived from chemical or mechanical or nuclear particle interactions. "Organic energy" then is the usable power derived from carbon-based chemical interactions.
The exercise of how much energy can be usefully derived from physically breaking down a human body, without the use of antimatter, is left to the reader. The calculation of how much energy is present in the visible area of the Crucible particle beam alone is also left to the reader. hint: it's orders of magnitude more than can be derived just from the human body. Second hint: orders of magnitude are powers of 10. not multiples, exponents.
The idea that shoving a body into a massive particle beam accelerator will somehow fundamentally change the qualities of that particle beam accelerator into something that can change all life in the galaxy is.. it's.. indescribably ludicrous. It's like claiming that shoving a potted plant into the heart of a blast furnace will somehow make steel that can talk, grow, regenerate and heal itself.
I'm not even going to get into the "DNA" of synthetic life. That's beyond nonsensical and I'm pretty sure that it's a case of "Tech the tech." "But captain, we can't tech the tech, because the tech will tech catastrophically. Maybe if we use the tech to tech the other tech, by attaching the tech..."