You can't really put the president stepping down only on Messi's decision. He's had an absolutely terrible time there, overspending on a very imbalanced side, both age-wise and positionally. They need to sell to buy, the situation is dire and they've suffered the most embarrassing defeat in recent history. It's a culmination of a nightmarish reign and he should rightly step down. Instead he decided to go to war with Messi in the press, and whilst that would be OK if he'd have been remotely competent in the first place, there's only one winner when you've proven yourself a catastrophic failure.
I also wonder if a structural change at Barca is enough to convince Messi to stay. It's almost impossible to imagine they could challenge for the CL in the next few seasons given their current squad and finances. It's going to be a painful rebuild.
I'd quite like to see him move (of course to us, but that's not realistic).