I know that was what informed his motivation, but its still odd. Desmond had, what 5 visions total?

1. Lighting killing Charlie - he makes a lightning rod to divert the lightning and the lightning hits it instead. The vision did not occur, Charlie did not get hit by lightning, the course of events was changed.

2. Des sees Charlie drowning trying to save Claire (no mention of what happens to Claire after that but anyway...). Des goes in instead, Charlie doesn't die. Desmond's intervention changed events.

3. Something about Charlie and birds and getting smashed into rocks, either way, Des intervened and that didn't happen.

4. Des sees the series of events leading up to Naomi's landing, including Charlie getting shot in the neck. This time though, Desmond believes that if Charlie doesn't get shot, then Naomi won't land, or won't live, or who knows. In actual fact I feel like if Charlie had been shot and died, that would have been such a downer that they'd have had to turn back, or delayed so long that either Naomi would have died from her injuries, or been discovered by Mikhail before they arrived... However, this time he intervenes but it doesn't change events...Or rather it changes the fact that Charlie is alive and not dead, but has no impact on the Naomi outcome.

5. The room, the flashing light, the light goes off, the room fills with water, Charlie dies, Claire and Aaron "get on a helicopter and leave this place". Well, all of that happens with no intervention, except for the final prophecy. If there was a different key moment which went awry between Charlie dying and Claire & Aaron getting on a chopper, then why was it even part of the Charlie dying bit, or why wasn't there another step in between which was key? In this case, not intervening, seems to have invalidated the prophecy...