There are couple of ways of doing it. I believe there is a remote control that you can get that will disable it, but I never bothered with it because I like combat in the game so I always fought him.
In Enhanced Edition they've made him harder though and I was stuck on it a few times, I almost don't want to spoil it for you because when I figured it out and beat him it was a great feeling.
Basically what happens is the two mages shoot lightening at it which charges him and on his next turn he will shoot a very strong lightening that will one shot whoever gets hit. If you can notice there are 3 levers in that room, kind of in front of him. One is on the left side and the other 2 are on the right side. What you need to do is flip each switch before its his turn which will discharge him and he won't be able to do the lightening attack. He'll still shoot something but you should be fine. You have to do this every time the wizards charge him so keep one of your characters next to each lever at all times until you kill the wizards. After wizards are dead you should be fine. If you get into melee range with him he actually has a pretty powerful melee attack, so you might want to watch out for that. Also don't shoot lightening at him, it will also charge him. My party that I went in with was 2 melee characters, Jahan and the Wild girl who I use as a ranger. She did a lot of the damage.
Also you can effect some status effects on him as well, I think he can be knocked down or frozen, I can't quite remember, but I remember that I was able to take him out for a few turns. I have a feeling he might be shocked as well, but than you have to do the lever thing as well.
I don't know if there is an order of how to pull the levers, but what I did was Left one first, than the one accross from it than the one on top which is the closest to the robot.
Hope this helps.