He could have turned himself in. He had that right didn't he? I don't think the Constitution protects people, even citizens, who join an organization that openly declares and wages war on us.
You are mistaken.
Article 3, Section 2: The Trial of all Crimes, except in Cases of Impeachment, shall be by Jury; and such Trial shall be held in the State where the said Crimes shall have been committed; but when not committed within any State, the Trial shall be at such Place or Places as the Congress may by Law have directed.
Article 3, Section 3: Treason against the United States, shall consist only in levying War against them, or in adhering to their Enemies, giving them Aid and Comfort. No Person shall be convicted of Treason unless on the Testimony of two Witnesses to the same overt Act, or on Confession in open Court.
The Congress shall have power to declare the Punishment of Treason, but no Attainder of Treason shall work Corruption of Blood, or Forfeiture except during the Life of the Person attainted.
Amendment 6: In all criminal prosecutions, the accused shall enjoy the right to a speedy and public trial, by an impartial jury of the State and district wherein the crime shall have been committed, which district shall have been previously ascertained by law, and to be informed of the nature and cause of the accusation; to be confronted with the witnesses against him; to have compulsory process for obtaining witnesses in his favor, and to have the Assistance of Counsel for his defence.
All of these provisions specify the rights of people accused of crimes, including treason, which is very carefully defined. And merely joining an organization that openly wages war on the U.S. is not a crime; one must actually DO something of a material nature for them, or of course wage war on the U.S. oneself.
Of course, treason is a crime that can ONLY be committed by a citizen.
Historically, we have an example of those who waged war on the United States (in the 1860s) but were not denied their rights, including the right to receive a pardon at the discretion of the president, which they did.
I don't really know if any of this applies to the person in question (who hasn't even been named that I noticed!), but if it doesn't it's because he was killed in a war zone, not because being accused of terrorism causes someone to forfeit their rights.