I don't think it's ever been shown conclusively that he's working in everyone's best interests. His motives are portrayed as ambiguous because they are. He often works to save the lives of the crew, but that is likely because he needs them as much as anything else. I don't think he knew that Destiny would recharge in a star either, but I don't think he was all that surprised when they didn't die either. I think he suspected that they wouldn't, and knew he couldn't control it either way. That's why he was relatively calm about it all, and suggested Greer take TJ's place on the shuttle, who at the time he fucking hated.
Ultimately we still don't know what Rush's true motives are. He talks about uncovering a cosmic mystery to rouse the crew, yet at the same time lets slip language about gaining power to "right the wrongs". I would not be surprised if he was looking for a way to ascend and/or bring Gloria back.