Jesse is absolutely the sympathetic character now. After Gale's murder he has been completely horrified with himself and consumed by guilt. He is constantly trying to find a way to reign Walt in, mainly to preserve his own sanity.
I definitely think their individual reactions to Landry/Todd's act will be the beginning of their rift. Walt will indirectly approve of what Todd did, maybe not explicitly but in a "what's done is done" type of attitude. Whether or not Walt would have made the same call, he will acknowledge that the outcome is favorable for their operation. ("Nothing stops this train. Nothing.")
Mike has seen through Walt this whole time, but Jesse can't see him for what he is due to admiration and loyalty for his teacher/mentor/partner. But if Jesse finds out even a fraction of the things Walt has done to him, he'll understandably despise him and want him dead.