Yes. If Neo had the powers ascribed to him at the end of the Matrix he should have been able to simply remove any weapon, person or obstacle in his way.
He should have been able to wake anyone and everyone up. That would have led to the deaths of everyone tied to the matrix in the real world. That was the actual problem. No matter Neos powers in the matrix how was he supposed to save millions of people in a blasted post apocalyptic world with limited food and resources.
Eventually working with the machines was inevitable, they just could have gone about it a different and more satisfying way.
I remember reading a far better idea (written after M1) for how the Matrix movies would/should go in the form of someone's prediction of what the ultimate plot twist would be. It was a far better idea than the actual result was (admittedly, not that difficult to achieve). I wish I could find it now It revolved around the idea that Zion is a matrix in itself, and anyone who has "woken up" is actually connected to another matrix being Zion and are just other AIs, and Zion has its name as a result of language evolution, originally being 'zero one'. IIRC, all humans died in the war that 'the second renaissance' (Animatrix) mentioned, and the name of the city comes from there. I don't remember all the details, like why there would be a matrix in the first place in that scenario, but anyway. The author had a disclaimer that he would deny everything if his prediction turns out to be wrong, but I did track it down at some point after Revolutions was released.