There are a number of complexities that come together that make the claim that President Trump violated obligations under the Geneva Convention difficult to justify.
By definition, the Blackwater employees were not mercenaries according to the Geneva Convention (United Nations Mercenary Convention).
Among other things, the Geneva Convention requires that a mercenary
is neither a national of a Party to the conflict nor a resident of territory controlled by a Party to the conflict
The Blackwater employees would have been considered civilians according to the Geneva Convention.
Although civilians can be considered combatants according to the Geneva Convention in International Armed Conflict, by the time of this incident in 2007 the situation in Iraq was no longer considered International Armed Conflict and it's questionable if the Geneva Convention applied. (The status of the conflict changed with the handover of sovereignty on June 28, 2004.)
The incident that occurred, often called the Nisour Square massacre, was related to Blackwater employees who were guarding a convoy of U.S. State Department employees. In essence, the Blackwater employees were acting as private security guards, not as active participants in armed conflict. As civilians, the employees could have been charged under Iraqi law or U.S. law for the actions they took that day. However, under the Coalition Provisional Authority, U.S. contractors were not subject to Iraqi legal jurisdiction without the permission of the U.S.
From a CRS Report for Congress titled Private Security Contractors in Iraq: Background, Legal Status, and Other Issues:
Under CPA Order Number 17, as revised June 27, 2004, contractors shall
not be subject to Iraqi laws or regulations in matters relating to the
terms and conditions of their Contracts...
This left U.S. law, specifically the Military Extraterritorial Jurisdiction Act of 2000 (MEJA), as a means to prosecute the Blackwater employees for any potential criminal acts and it is under this law the Blackwater employees were ultimately charged and convicted. MEJA
allowed persons who are "employed by or accompanying the armed forces" overseas may be prosecuted under the Military Extraterritorial Jurisdiction Act of 2000 for any offense that would be punishable by imprisonment for more than one year if committed within the special maritime and territorial jurisdiction of the United States.
The Blackwater employees were not charged for "war crimes" under the Geneva Convention but for manslaughter, attempted manslaughter and a weapons violation.
Now to the question of President Trump's pardon legally violating the obligations of the Geneva Convention.
Assuming that the Geneva Convention applied to the Blackwater employees and their actions at Nisour Square, from a U.S. perspective a treaty cannot alter the President's constitutional powers.
The second article of the Constitution of the United States, in Section 2, states:
...he shall have the Power to grant Reprieves and Pardons for Offences against the United States, except in Cases of Impeachment.
The law upon which the Blackwater employees were convicted was U.S. law; an offense against the United States and, therefore, a pardon for a conviction under this law is within the President's constitutionally granted powers.
In Reid v. Covert, the U.S. Supreme Court made it clear that treaties cannot alter constitutional powers:
It would be manifestly contrary to the objectives of those who created the Constitution, as well as those who were responsible for the Bill of Rights -- let alone alien to our entire constitutional history and tradition -- to construe Article VI as permitting the United States to exercise power under an international agreement without observing constitutional prohibitions. In effect, such construction would permit amendment of that document in a manner not sanctioned by Article V. The prohibitions of the Constitution were designed to apply to all branches of the National Government, and they cannot be nullified by the Executive or by the Executive and the Senate combined.
There is nothing new or unique about what we say here. This Court has regularly and uniformly recognized the supremacy of the Constitution over a treaty.
The pardon issued by President Trump was legal from a U.S. law perspective. As such, it represents an official action of the United States. This would leave it to the United Nations to determine if the U.S. was in violation of any treaty. Given the difficulty in establishing that the Geneva Convention even applied to the actions of the Blackwater employees it seems a stretch to think that the U.S. would be found in violation.