The question of the Prime Directive here is rather... dubious.
Did the crew have it within their right to repair the monument?
Maybe that was considered interference.
On the other hand... deploying buoys to warn other ships on what to expect probably could have been done in the first place by the species who placed the memorial.
Perhaps the Voyager crew was traumatized so much because the memorial was damaged (due to being neglected - and I think it might have even been implied) - perhaps if it was functioning properly, it wouldn't cause the crew to be considered 'violated'.