Here are the major consequences:
As noted in the question, the Empire must now defeat all Rebel forces on the Rebel Base (as opposed to just all Rebel ground forces) to win the game.
The "Bombardment" tactics card becomes useless for one side in ground combat.
The "Crippling Blow" and "Liberation" objective cards become harder for the Rebels to accomplish, although these are often achieved through "Incite Revolt", "Public Uprising", or "Lead the Strike Team", which are unaffected.
A system with a Death Star is now unassailable on the ground until you get the "Death Star Plans" objective (although making such an attack would be an odd move as the rebels).
In the "Rise of an Empire" expansion, an Imperial system with a Death Star and Shield Bunker becomes completely unassailable to direct attack, and can only be taken via a mission card (such as "Lead the Strike Team").
A Rebel system with ion cannons is harder for the empire to take
As an aside, the empire already needs to win the space battle as well as the ground battle for the rebel base in order to win the game. Note that the rules for winning as the empire refer to "units" in the system, which includes space forces:
The Imperial player wins the game immediately if there are Imperial units in the Rebel base’s system and there are no Rebel units in the system.