Is that really true to that extent though? The defence seemed to be the worry going into the tournament, but against France sepcifically they controlled the majority of the match and while France had some dangerous counters, there weren't that many either. The deciding goal being a good counter but an unfortunate own goal. I think it's unrealistic to expect a team to completely nullify a team like France over 90 mins. Germany's problem was more that they couldn't create enough good chances.
This game against Portugal was a bit more open, so they did concede some chances and openings too. However their attacking had much more intent.
I think as long as they can continue improving their attacking cohesion in the following matches defensive weakness shouldn't be that big a problem. Can't really imagine many teams will be able to dominate midfield or possession generally against Germany. It's just a question of them turning that into quality chances.