(Our pastor preached on this passage this week, dealing specifically with leadership; you can listen here.)
How do we deal with God's presence and His absence? It's much easier to choose one or the other and stick with it. One route is to chant "God is good, all the time" to the exclusion of the broken world around us, the pain inside us, and even Scripture itself (which, while it supports God's goodness, doesn't include this phrase and would certainly critique its use to drown out reality). Another is to act as if the discovery of His absence somehow negates faith—questions like "why do bad things happen to good people?" usurp God's sovereignty; His authority isn't recognized unless questions regarding His absence have been answered to our satisfaction.
It's certainly OK to struggle with the ways in which God is absent. In fact, it's dangerous to avoid it. But the discovery of His absence is by no means revolutionary—Jesus taught about it two millennia ago—and doesn't diminish who He is in the least. Both His presence and absence are to be part of the fabric of our faith. For me, there's great freedom in realizing that I haven't uncovered Christianity's deep, dark secret by wondering where God is. There's humility in it, too. And, perhaps most preciously, there's hope.