They leveled most of the galaxy, shoot down ships and people die in droves like in the beam run, TIM tries to to block you on their behalf and that´s "they don´t fight back?" But telling Shep where to find the destroy button with the addition of "Oh but I will take your synthetic friends with me, BWAHAHAH" is?
In the original ending the catalyst says:"You can destroy all synthetic life if you want, even the geth. And you are partly synthetic." No mention of technology, mass relays and stuff. If you killed the Geth, there´s only EDI left and hm well, I like her. but galaxy or one squadmate? EC adds technology will be affected, losses will be there but the survivors will be able to repair it quite easily. Probably differs on EMS. But if your EMS is lower, the Catalyst still shows you the way and something raises a walkway so you can do it, even when destroy is the only option.
If it was playing some kind of desperate final manipulation game it wuld leave out the destroy option or even simpler not raise the lift, pop the oxygen bubble surrounding the decision "chamber" or not talk to you at all. Shep only wakes up after the Catalyst says wake up/why are you here. The catalyst can wait if Shep decided to nap some more. Perhaps Its Reaper minions can blow up the Crucible in the meantime
As it is the Catalyst probably suffers from some Crucible malware inserted into its code. If it was fighting you, it wouldn´t activate the lift or talk with you, it would call in reinforcements. There are probably some on the station, mopping up the residents, looking for hiding organics. If the catalyst was convinced that "uh yeah, my solution isn´t viable anymore", there is no reason to continue harvesting or insisting that you use the Crucible for the options.
If you cut out the whole catalyst stuff the Reapers are actually fighting back more, compared to leaving the exposition piece in.