There's somethings that I kinda agree with the 'whys' to accept it.
First, for me Instrumentality was morally corrupt because it was enforced upon people, SEELE and NERV never wanted to give to humanity the choice to reject it, neither the choice to or make part of it or not make part of it, beyond all destruction and manipulation needed to perform it but in a scenario where neither of these things happen, I would actually see it as morally superior, it is a way for the weak, after all, those that get the worst things, those that will lose, those that can't deal well with people, those that lost in life, those that are handicapped, those that are alone, those that can't deal well with pain, it is an exit and frankly? I find the calls of accepting such a exit as 'cowardly' kinda...unrealiable, because first, suicide (if you do see Instrumentality as suicide...) is a pretty hard thing to do, survival imperative after all, it is way stronger than you think it is.
Choosing an exit isn't a coward choice, after all, it is only cowardly if you're going to damage others to do that so...whoever says that it is a coward way to go needs to answer 'why exactly it is a coward way to go' and particularly? I dare ya to anwser it.
Second, no matter how much we try, somethings in the world just boil down to 'You're not pretty' or 'you're not the best' and if gave the choice, at least in romantic love (and in various situations...), your partner (Or an employer or acquantances...) will eventually run or accept to whoever is smart, beautiful than you and you will be dismissed, the world and the universe isn't fair, people need to accept it, it isn't too much complicated, it is pretty simple actually, but no big deal, maturity is to accept such things and live with it (Obviously, considering that there's way, it wouldn't be immature to accept it...immaturity is to try to live a dream in reality...principally because reality eventually beats upon you and makes everything to crumble down.)
Third, Art? Music? Creativity? Those things only ended up coming to be because we kinda need those to survive? if we don't needed those things, because we became a god like being...why exactly would those things be needed? We don't need to use a hot iron rod to treat wounds because we managed to create a better thing to deal with those things, it is the same thing here.
Fourth, drive to sucess, right, one can say that my reasons boil down to this, before anything, it isn't because I believe that improving is a bad thing, never, if you do exist as an individual, you should actually improve yourself (and if possible improve your body, I am a transhumanist for a reason), but if you do exist as a god...why exactly is it bad that you wouldn't improve? We improve because again...we need to improve, but if you don't need, why exactly would do you do it? Maybe by a inner wish? I don't care, but then, my reason, some will improve and will win, they will reach happiness and sucess, good.
But others will never reach those things and unless if we're willing to violate people's freedoms, they will need to bear with it and accept what they can get from their efforts, even if they were pointless...
And fuck that, if there's an exit from such pain, there's nothing wrong with it, at least there will have not pain and suffering by envy and bitterness from defeat.
That would be my reasons to accept Instrumentality.