Well, yes... and no. Parliament is sovereign; it can pass whatever laws it wants. That does not mean that every law is a good idea, or (more importantly, from the Tribunal's perspective) in accordance with the Treaty.
To point out the obvious, Parliament was sovereign when it passed land confiscation laws in the 1860's. It had every legal right to pass those laws. But they were clearly in violation of articles two and three, and there is now widespread acceptance that they were wrong.
And to point out the equally obvious, the Waitangi Tribunal is not a court, and its judgements are not binding. That does not mean they should be ignored. The Tribunal's report should make the government pause and reconsider whether it is doing the right thing. If it gets this wrong, it will haunt us for the next twenty years.