If Jesse is caught or investigated, Gus' entire operation ends though; that concern is far more important than any concern over Walt. He cannot afford to be careless, yet employs someone who is a complete liability. And while Walt is a certainly unpredictable, his responses to Jesse's death would be limited. He can't quit, go to the police, or kill anyone of importance in the operation.
Considering Walt will probably have to deal with cancer again eventually, Gus already knows Walt is not a long term investment; he'll have to replaced eventually. Jesse isn't trustworthy enough to take over, and Vincent is dead. It would make far more sense to start looking for a new partner for Walt, to learn from him and continue the work in the event of his demise.