Actually I have a hunch how this might go. Two really.
Here; you have a weapon that can kill Reapers. Go do the 'refuse' option. Here's your Star Wars Death-Star-Blows-Up
ending, now shut up about it.
Here; you have a weapon that can kill Reapers. Go do the 'refuse' option. Hey look; you almost won!
I bet you if you buy a few more future DLC story quests with more legendary weapons
you might actually win someday.
Either way...I dread those options. As I said before, I actually like
the idea that you can't always kill space Cthulhu.
I agree completely, I was suspecting something like one of these two scenarios. I'd ACTUALLY be okay with that. It allows them to maintain their original narrative vision (whatever the fuck that was) while still appeasing EVERYONE.