Agree that if the rebels win the ground battle before Palpatine can retreat, the card should definitely work. As for the rest, it's ambiguous. Making things even more complicated, the rebels played Jedi Luke Skywalker and the card also states "If Luke Skywalker (Kedi) is in this system, eliminate 1 imperial leader in this system" (emphasis mine).
So my interpretation of everything, and maybe this is hypocritical, is that when Palpatine retreated, the rebels won a battle in Palapatine's system, even though Palpatine has since fleed it, so they do receive the two reputation points. However, Post winning, there is no imperial leader in the system, so the rebels do not get to eliminate Palpatine.
Does that make sense as an interpretation or should it be all or nothing?