Psalm 69 is David praying to God about his enemies that are more numerous than the hairs on his head. He is fearful lest others who love God suffer because David is known to love God and is in disrepute. It is because of his zeal for God that he suffers.
Verse 9, quoted in John 2, comes in that context. David has zeal for God’s house, and because of that zeal he is suffering as he is. So, “consume” does not just mean “absorb”, in the sense that he is consumed with passion for God’s house. Rather, his zeal for God’s house is eating him up; it is leading to his mistreatment.
So in John 2 the disciples call this Psalm to mind. John does not say explicitly whether they called it to mind then and there, or whether (as in verse 22) they made the connection later. Applying Psalm 69:9 to what Jesus does in John 2 has two effects on the way we see Jesus’ actions. First, Jesus (like David before him) has zeal for God’s house; he cannot stand by and watch as the temple is abused. Second, that zeal will be consuming. Notice that the tense has changed. In Psalm 69, David reports that zeal for God’s house has consumed him, and that is why he suffers. In John 2, the tense is future. The zeal that Jesus shows in the present will consume him.
This means that, as with Jesus’ pronouncement in verse 16, we are being led to think of Jesus’ death. This confrontation with the abuses of the Judaism of his day will ultimately destroy Jesus. However, (verses 19-21), it will not destroy God’s true temple or Jesus because what is destroyed will be rebuilt as Jesus is raised from the dead.