Yes all choices are forced on you, but how they are forced is the difference. The narrative difference of the plot device used in this end vs you have a fleet in reserve how do you use them is different. Its a game so you are only going to get a finite number of choices, but how they decide to deliver the package makes a difference.
The Crucible was well delivered IMO. For the entire game, no one knew how it worked or what it would do, we only knew that it was some sort of energy source and that it exploited the technology of Mass Relays. They don't have to tell you earlier in the game that you'll have to pick between Control, Synthesis or Destroy.
As for the monumentally stupid part, of course its just my opinion. But there is a vast difference between a little bit of space magic and the endings which are massive amounts of space magic which don't fit the established space magic.
Isn't a game series allowed to introduce things to the players in a later game? Just because you didn't know something before, doesn't mean it's not possible. The Crucible/Catalyst (not the Intelligence, the actual Catalyst aka the Citadel) is technology that we don't fully understand because our cycle doesn't have that kind of technology. Well, I could even say that we actually do have that kind of tech but in a smaller way.
In Control, Shepard's corporeal form is destroyed, but his mind is uploaded as the new Reaper master consciousness. The Virtual Alien were able to upload their minds in a virtual world (in supercomputers) and that was about 8 000 years ago (from 2185).
For Synthesis, we can't achieve it any other way, so we don't have that technology.
In Destroy, if the energy from the Crucible actually works by overloading Synthetics like I said earlier, then we also have that technology but on a way smaller scale. The Crucible connected with the Mass Relay network allows it to be galactic wide.