Accept that the Barca defence is below par for a top club and get the rest of the team to work harder to protect them. Essentially what Sabella did with Argentina in the World Cup. This would mean sacrificing their current playing style and preferred positions for the superstar players.
It may seem like an unrealistic solution but look at frikking Real Madrid's midfield - James Kroos Modric Isco. Possibly the most lightweight midfield 4 among any top clubs. But Carlo got James and Isco to radically change how they play and sacrifice their natural instincts. They also have the tactical flexibility to switch from a 4-4-2 to 4-3-3 depending on the game situation. However, I don't see the same hunger and quality in the Barca midfield to adjust and prove themselves. Rakitic is OK, but you're gonna find it really hard to change Xavi, Iniesta, Sergi Roberto or even Busquets' style of play.
Mascherano in midfield would be the first step, but not in a 4-3-3. Also going to need a lot more defensive work from Messi, Neymar and Suarez. Barca's right flank was exposed in the first half because Xavi and Suarez made no efforts to support Alves. The same thing happened last Clasico in the Bernabeu when Neymar let Di Maria have the game of his life against Alves.