The nerf makes sense using this train of thought:
Problem: Her Q/E and R/E combos are too reliable for the damage they do.
Potential solutions:
Nerf the damage, but keep the reliability. Consequence: You lower the reward for playing Anivia well. Meh.
Nerf the reliability, but keep the damage. Consequence: She keeps her reward for being played well. Her core combo remains as powerful as it is, but edge cases where she barely tagged you with Q or R at full range and still got a full-power E off are removed. Feels a lot better to play against (less bullshit), and solidifies her mid-long ranged character. Remember, unlike the other long-to-extreme range champions, she has no mechanic that makes her come closer to you than necessary.
Overall, after giving it some thought, I think that this nerf is a good nerf that keeps the core character intact.
From playing Anivia myself, and one of my friends thinking he is Froggen junior, I know that the window during which you can combo an E onto R or Q is sometimes rather BS. Example: Hitting someone at full range, taking a moment to decide to move in to E, barely getting in range due to the slow with the target in retreat after the stun, enemy is still moving away while E is in flight, but takes the double damage because the window for it is so long.