season 4 follows your basic parallel story structure: Walt becomes paranoid that Gus is going to try to kill him. Jesse becomes wrapped up in Gus’ cartel problems. The two plots become entwined when Walt assumes that Gus’ reason for giving Jesse attention is to orchestrate Walt’s death, and things escalate from there. This is all directly addressed in “Bug,” when Gus tells Jesse (and from the context of the rest of the season, he appears to be telling the truth) that he needs Jesse to learn the formula to teach the cartel, not to kill Walt.
Gus is a pragmatic and intelligent man. Obviously he only tried to kill Walter in “Full Measures” because of the escalating drama with Jesse and Gale – but that’s all in the past and, starting with Victor’s death, it would be in everyone’s best interest to put the past behind them.
Now, Walt may be suspicious of Gus, but if Gus would just explain the situation with the cartel to Walt he probably wouldn’t be so quick to jump the “he’s gonna kill me” assumption. If Gus would have just told Walter what was going on, they all could have gone on happily making meth until the three months was up, at which point they go their happy, separate ways.