Since I poisoned the big fish and was kicked out of Manaan (they say that I can't ever go back). Is there any way to overcome this and open the spaceport doors and get back in?

that's why once i started over, I left manaan to be the last place i finished.

if you pick blow up the machine instead, they wont kick you off manaan

Just do all the sidequests before that, there is no use going back afterwards anyways. ;)

No kiddin, here's how you do it. This works especially if you wanna do the missions, then come back to the Manaan Glitch later.

Dont poison the shark, blow up the equipment. Then during your trial, admit to blowing up the equipment that was put down there by both governments. Then tell the judges you did it so as NOT to kill the shark. The shark is some kinda religious type thing there. Then you will be found innocent.