I don't see how it matters if it was done in his best interest. If you give someone a million dollars because you'll get something better for doing it, it doesn't make that act of kindness any less beneficial. Walt may have done some of those things because he too benefited from it, but there shouldn't be any doubt that he cared for Jesse. Even after Jesse doused his house in oil, Walt was still the ONLY one who said killing Jesse for it wasn't an option. He really cared about the kid, and all the way up to the end, refused to believe he would snitch on him. The only time he decided to take Jesse's life was after Jesse threatened to get him where he really lived, which I believe Walt took it to mean his family.
And his actions in the recent episode where because instead of facing him like a man, Jesse went to the DEA and brought Hank into the crossfire which ultimately got him killed. Leaving Jesse to the Nazis and telling him about Jane was his revenge for Hank's death and the loss of 70 million dollars that he had made over the years. Just like Walt is unable to let go of his pride, Jesse was unable to take the good things he'd been handed and walk away. By coming back and snitching to the DEA, Walt lost everything he worked for (including his family) and Hank lost his life. And all this after Walt defended Jesse and his honor to the very end. Even when he knew Jesse had to be put down, he said that Jesse isn't a snitch, he's only misguided, and was family to Walt. I'd say it's understandable to rub salt in that person's wounds after you save them, help them, defend them, then they come back at you to ruin your life, legacy, and family. Anyway, sorry for the tl;dr. I was just bored, and this show is fun to discuss. I apologize if I seem abrasive, it's just the way I type. I enjoy talking about BrBa with you guys.