But the Arms would still influence him a lot more than they did in SM2
If I wasn't completely put off by your idea before, I am now. The arms couldn't influence him any more than they did in SM-2. Their sole function was to control and sustain fusion. So, they had to make Ock believe he had not failed in his calculations. They played on his ego and passion for his life's work.
Since he overcame their influence, and realized the error of his ways, going back to the arms influencing him again would be a huge step back for the character.
instead of Doc fighting with the arms he would basically get along with them.
Ummmm that's what happened in SM-2. He never fought with his arms until the end, when they resisted his instructions to release Peter from their grip.
He completely succumbed to their influence. He was a broken man who had lost everything. So, when they offered him a glimmer of hope that he had not failed with his dream, it was very easy for him to believe them.
We already saw at the demonstration that he was not opposed to violence to make his dream succeed, when he smashed Spider-Man into the wall when he tried to unplug the reactor.
I loved SM2, but Doc Ock has always been a straight up villian in the comics, so it was a little disappointing to see him be more of an anti-hero in SM2, do you follow.
Nope. Because he wasn't an anti hero in SM-2. The Punisher is an anti hero. Venom is an anti hero.
Ock wasn't. He was being selfish by rebuilding his life's work, making his dream come true at any cost, by hurting, killing, and destroying anyone and anything that stood in his way.
Drowning his reactor does not make him an anti hero. He was merely righting the wrongs he had done. Making up for his own sins.