Given the talk of Petraeus becoming Secretary of State, and the fact that he is still on probation, can't Trump just commute his sentence?

I don't have any mercy for him. He wouldn't have any mercy for me if I did what he did. Trump needs to wait until he serves his probation time and let him earn his honor and future security clearances.

It would be more logical for President Trump to issue a pardon.
Having said that, while GEN Petraeus is a good man, I think we would all be better served if he remain outside of government. What he did was highly questionable, and set him up to be compromised. He knew better, and did it anyway.
Not the kind of cat I want in a position of trust. More of an informal advisory role would make more sense than elevating him to a cabinet position, but I think he should play golf and give speeches.

Given the lady Senator is philosophically opposed to Gen Mattis as SOD she would probably have a stroke at the suggestion of appointing a compromised adulterer as the nation's SOS and voting to waive the 7 yr delay period to boot. Trump could of course commute/pardon his transgressions, probably not a big deal with POTUS elect's personal values, but would expect some pushback in Congress.