I'm no expert, but I think the writers did manage to muddy the waters with the phone call in "Beachhead", though.

If Landry has to get Jack's permission to transfer Sam back from Area 51, then he is still in her chain-of-command, and fairly directly so - he's making decisions that affect her professional career in a big way. So on that basis, a sexual relationship would presumably still be improper.

You could probably handwave it and say that the phonecall was informal or a courtesy thing, though.