It was part of the national territory following annexation. One shouldn't use 'always' when talking about a foreign nation forcibly overthrown and annexed by the United States.
I doubt that the 'whole of the Constitution' applied during the years of Martial Law following Pearl Harbor.
One could make the argument that Martial Law is sanctioned by the Constitution through Article 1, Section 9 which permits the suspension of habeas corpus. Furthermore, there is plenty of precedent for the imposition of martial law in the United States. Although, the Army's conduct in Hawaii was slammed in federal court after the war with a judge saying it "set up a military dictatorship".
In short, Legion is correct that, as an organized, incorporated territory Hawaii was on the path to statehood. My understanding is that no state was admitted without going through a stage as an organized, incorporated territory however short. So going off of that the only* way I can see to make Hawaii a Commonwealth instead of a State is for annexation to happen differently. As a thought on how it could happen how about Queen Liliuokalani swallows her pride and is willing to grant amnesty to the participants in her overthrow. She is restored by the Cleveland administration but with an increased US military presence in the Islands and American domination of the kingdom. From this point Hawaii becomes a de facto protectorate of the United States with the Queen enthroned but power firmly in the hands of the American and European business men. This isn't a stable shape of things and I see Hawaii being something of an American Samoa writ large. So Navy rule, possibly the forced abdication of the monarchy, lack of development, etc.
*okay there's always the option of Hawaii calling itself a Commonwealth instead of a State as a few states do. But while that would result in a Commonwealth of Hawaii it doesn't fulfill the OP now does it...