It's very good to see that real madrid has not yet lose its chance to win against barcelona caused by second leg is still available.
I would certainly not write off Real Madrid yet. This has happened way too often now that they were with their back against the wall and turned an ugly situation into a positive outcome for them. Now the game in Barcelona will be harder because chances are good that Barcelona has more players available by then. That is clearly a chance that Real Madrid missed today.
The game today says nothing about the game that will be in La Liga. It could have gone either way today as well. Modric's chance after 30 seconds could have been a goal, it was no off-side. Benzema could have timed his run into the box better and thereby avoid off-side when he scored that goal. Sometimes the own goal also doesn't happen the way it happened.
We are discussing about nuances here and even the Copa del Rey is not a done deal yet for Barcelona. Taking the lead in Barcelona is not impossible for Real Madrid. I would say that the chances are about 60:40 for Barcelona at this point.