Because (just like in NY with Trump, and specific charges) if a crime is committed within a state the state has the right to prosecute regardless of impeachment or federal charges. The UCMJ is technically federal law. But we’re looking at three different aspects of lawful charges for persons who might commit a crime per the Presidents order. The president could absolutely pardon the persons involved. But only at the federal level. There’s nothing stopping the state or states from prosecuting the same individual. It’s not just one set of checks and balances is my point. The department of justice can also bring charges regardless of UCMJ tribunal (Court Material). Which is really where double jeopardy should kick in but doesn’t for service members.
Additionally and most importantly actually, a court martial conviction for murder would result in a dishonorable discharge from the military. That can’t be overturned by a presidential pardon. They would lose their benefits. Medical and so on. Pensions. It’s a cost benefit analysis at that point. They don’t just get to walk away no harm no foul cause presidential pardon.