"Lift up thy weapons. For you are my soldiers, and must you be steadfast, strong, and brave of heart. They who neither hesitate nor stumble shall be rewarded. Then shall you have glory. Then shall your deeds be remembered for eternity." - Balthazar
Balthazar's Rest hasn't been completely untouched by Mordremoth, but the inner chambers remain intact. The buildings, once ornate, are now weathered and overgrown. Despite this, and the change of the land formations outside of the temple, Balthazar's Rest remains nearly untouched in the second game.
Again, as I've mentioned in another post before, I have a theory that humans in the first game saw their creations through rose-tinted glasses. In the second game, we get a chance to look at nearly pristine replicas of the land 250 years later. We see that they're not quite as ornate or spectacular. While this can be chalked up to a difference in design aesthetics on the Guild Wars teams between the games, I prefer the idea of an in game, lore-related reason.
The Temple of Balthazar can be found in The Falls area in Guild Wars in the bottom left of the map. Likewise, Balthazar's Rest can be found in the bottom left section of the map in Guild Wars 2. It's easy to navigate the two locations once there; they've done an amazing job replicating it in Guild Wars 2.