Who would we pick in the place of Rahane? Rayudu is no better, Kedar Jadhav and Uthappa could bat 6/7, but not at 4. Pujara might do slightly better, but he lacks a 4th gear too, and then there are the unproven young 'uns like Pandey, Iyer, Gurkeerat, etc.
Rahane is still comfortably one of the top 6 batsmen in India. He deserves a spot in the ODI side, He didn't play that awful an innings today. He supported Rohit, he set a platform, and he just got out when he was looking to push on. That happens. There are 4 other batsmen in that top 6 who didn't contribute. If you've only got two batsmen crossing 31 you aren't going to win many runchases.
Figuring out a number 7 is a more pressing issue, especially since MSD can't seem to find that top gear anymore. We need to either find a legit batsman who can contribute with the ball too, or get the part-timers working on their bowling and stick another big-hitting batsman in there. Axar/Binny aren't going to cut it.