If they were programmed for evil though, then wouldn't Zidane have evil tendancies as well, given he was made to replace Kuja?

It's more Kuja was "Raised" to be Evil, while Zidane was not.

And Kuja didn't do the things he did against Garland to be evil, he did it for various other reasons. IE - Inferiority complex, Narcissism and the denial of his fate.

And he tried to Kill Zidane just before if you remember.

In the end I think Kuja saved Zidane because he had already failed. He could not deny his fate so any further struggling was useless.

Given that, Zidane is still his brother. And while his own ends could not be met anymore, he decided to use what energy he had left to save Zidane.

So saving Zidane didn't make Kuja any less evil, it just shows he's not all bad.