In Season 3 Gus sets up Walt and Jesse in the fully equipped laboratory to make meth. Gus is a rational and self controlled business person. He runs his empire in the understanding that a tiny mistake might result in either law enforcement catching him, or a rival cartel killing him. He expects all his employees to act in the same manner - this is a business, and everyone should be professional.
When Jesse becomes a liability and Walt stands by him, they have both become a danger to Gus personally. At the beginning of Season 4, Gus is forced to continue to use Walt as his cook, but he has clearly identified him as a dangerous person, too intelligent to easily outwit, too unreliable to trust. Unfortunately parting on bad terms when you are in a highly illegal business is not really an option. At any point in the future Walt could give evidence to the authorities about Gus, or if Walt continued to cook on his own and ends up being caught by rival drug lords, he could be used to get back at Gus. Firing Walt and hoping he would keep quiet, even under threats to his family would not be enough for the ruthlessly controlling Gus - its no comfort to think that Walt might eventually suffer, if he's already in prison because of Walt's evidence.
Killing Jesse might have been an option, but Walt had proven quite loyal to Jesse and could not have been relied upon to have been unemotional and continued to cook for them. Threats to his family are only good if you think they will work. It only takes Walt to crack, go into witness protection and Gus is sunk. Walt could easily claim he was forced to work by Gus to plead for protection or a lenient sentence. Its Gus that has built an enormous drug manufacturing and distribution empire, not Walt.
Why did they take Jesse to help Mike? In my opinion Gus and Mike decided that they needed to divide Walt and Jesse. They decided that they could try to mentor Jesse, he's young and can be a little naive. Giving him almost a father figure to look up to and to make him feel like he is being trusted was a powerful psychological technique to use on him. The fact that he might be able to replace Walt as the cook was a secondary benefit.
