We do not naturally see how Jesus or his Father can weep over something they have willed to come to pass. This is an example of how our natural intuitions need to be adjusted by Scripture.
We naturally conclude, when we see God grieved or angered over something, that he did not plan for it to happen. But God’s ways are not our ways (Isaiah 55:8). We should adjust our thinking to the way God really acts.
For example, just this morning I read in my devotions these words concerning God’s judgment on the cities of Moab:
“I weep with the weeping of Jazer for the vine of Sibmah; I drench you with my tears, O Heshbon and Elealeh; for over your summer fruit and your harvest the shout has ceased.... I have put an end to the shouting.” (Isaiah 16:9-10)
Alan Harman, says in his commentary, Isaiah, “God expresses his grief over Moab, as he brings destruction on it” (137).
You see this by noticing the repeated word “shout” and “shouting”—the same word in Hebrew. “I weep...for the shout [of harvest joy] has ceased.... I caused the shout to cease.”
One implication of this, is that we ourselves, like God, may and should feel genuine sorrow over the miseries that come upon people because of God’s judgment. In fact, if we don’t, God may remove the ground of our gloating.
“Do not rejoice when your enemy falls, and let not your heart be glad when he stumbles, lest the Lord see it and be displeased, and turn away his anger from him.” (Proverbs 24:17-18)