I think the writers made that particular change because they didn't want to trivialize the cooperative action taking place between Shepard and Catalyst, not out of offense over players shooting him or disliking the ending. Shepard's personal organic-synthetic conflict is himself vs. Catalyst/Reapers, so Shepard turning physically hostile towards the Catalyst (as opposed the verbal hostility that triggers Refuse) should really be met with the same response from the Catalyst. You don't make progress on organic-synthetic relations by repeating the mistakes of past organics -- trying to pick fights with those far your superior.
On-topic, this is yet another out-of-world issue where I've found no good IT explanation: Refuse. They insist that Destroy is a rejection of the Catalyst, but to choose Destroy, you have to -- at bare minimum -- believe that the Catalyst indeed willfully points you to his and the Reapers' end, for whatever reason. That's still influence, from him to you. Refuse, on the other hand, is 100% rejection of Catalyst's influence. If there's any truth to the notion that indoctrination is taking place onto Shepard through the Catalyst, then Shepard should not accept anything from him, not even the promise of destroying the Reapers. And, also as of EC, Shepard cannot choose anything but Refuse if he/she remains hostile towards the Catalyst throughout the conversation. In the end, there's no way to choose Destroy without being at least slightly influenced by and cooperative with the Catalyst, no matter what one's motivations are. It's literally impossible.
And the IT explanation is "Well, you can't give up," but that again already assumes that any action by Shepard in that moment will change anything, an idea only planted in your head by the Catalyst (again, influence). It also assumes Refuse leads to failure, but what if BioWare decided to let it *somehow* result in victory, feasibly following the lore or not? Let's not kid ourselves: IT would be singing a VERY different tune.
So yeah, that's another out-of-game hole in IT, I haven't even dug my nose into all the in-game material that works against it...
See, this is just a misconception about IT.
In IT, the entire decision chamber sequence (at the very least that part), only takes place in Shepard's mind.
The catalyst wants only one question answered. Can Shepard be persuaded to see things from the Reapers' perspective, or does Shepard still want to destroy the Reapers?
That's all it is. Nothing we see happening in that chamber happens for real; Shepard doesn't actually shoot that tube, the Reapers aren't actually destroyed.
So it doesn't matter that the catalyst "offers" you destroy. He just wants to know if that resolve can be broken.
In refuse, you're worthless to him, because you don't want to accept the Reaper 'solutions', but you don't want to use the Crucible to destroy the Reapers either.
It's not about defying the catalyst. It's just about one thing: does Shepard still want to destroy the Reapers?
You're not "going along" with the catalyst at all if you pick destroy. All that you do is show that you still want to do what you set out to do.
Let's not forget that Shepard dies in every possible ending, even in most destroy endings.
Many IT-ers think it's likely that:
- If you want to control the Reapers, you will end up being controlled (maybe an agent, maybe a lesser Reaper, like a destroyer)
- If you want to destroy the Reapers, then you will end up being destroyed
- If you want synthesis, then Shepard's goal and Reapers' goal are aligned, and you've probably established the birth of a new Reaper.
Harbinger: "They will succumb and ascend, or they will be annihilated."
Only when you have an exceptionally high amount of war assets, Shepard survives destroy. This seems to indicate that Shepard had enough war assets to protect him/her.
Anderson: "Even the most experienced veteran is going to find themselves in situations they haven't trained for. In those instances, and there's more than I'd like to admit, your instincts are the only thing keeping you alive. That, and the men and women you're fighting beside."
And let us not forget the low-EMS destroy version. Where the only option the Catalyst gives you is to destroy them. I have never seen a satisfying answer from the IT-crowd on that one either.
Shepard does not live up to their expectations. Shepard didn't do everything he could to bring the fleets to the Reapers, didn't put much effort in making the Crucible the best he could. He failed as a leader, and isn't even worthy of ascension or useful as a Reaper agent. If destroy is Shep's only option, that means he destroyed the collector base, and thought it unwise to study the Reaper (tech). If Shepard had kept the collector base, that would mean Shepard was open to learning about the Reapers (like TIM), and therefore more easily corruptible. Therefore, if you kept the collector base, control is your only option.
If you have low EMS, the catalyst greets you with "Why are you here?". It speaks volumes. You're useless to him.
And when destroy is your only option, that just means the catalyst knows you can't be corrupted, nor does he want to, because you made no effort worthy of leadership. It doesn't matter to him that you want to destroy the Reapers, because it will only happen in your head, a beautiful vision before dying. In reality, the Reapers will simply destroy Shepard.