Why would it contradict an omniscient god? Consider being a mother/grandmother. Your kids squabble; do you always interfere, or do you think that it's important that they work it out for themselves? Sure there are limits, but we are limited to the physical universe, not an eternal one.
As Matthew 10:28 points out, one's eternal soul is what's most important.
Atheists love to point out that if God existed, then why did God allow millions to die in WWII? Over 250,000 to die in the 2004 Tsunami? Ergo, they draw the conclusion that God doesn't exist.
IMO, they are thinking only of the physical realm, not the eternal one. Both Matthew 16:26 and Mark 8:36 point this out by stating, "What good is it for someone to gain the whole world, yet forfeit their soul?"
IMO, God doesn't interfere in the physical world, but most certainly is there for the eternal one.