Side balancing was handicapped by this change. The ebb and flow of folks signing in and out is a constant. The ability to change sides to help even up sides is once every 12 hours.
I doubt it was handicapped. Plus, I think you're looking at things in snapshots rather than over the course of an evening. With short side switching, you'll probably see two phenomena: First, you'll almost always have one side with a major advantage. Folks like a winner, and they hate getting ganged, so you'll have a large proportion of players hopping to the "winning" side and exacerbating the imbalance. I suspect the number of people who hop to the largest side easily outweighs those trying to balance out the numbers.
Second, as the night wears on and people log in and out, the balance of power potentially shifts to another country. Suddenly you see major imbalances emerge as
that country has everyone flock to it in that time frame. So a short side switch doesn't necessarily equate to balanced sides, but rather leads to greater side imbalances in the short term and wild fluctuations in numbers between sides in the medium term (over the course of a night). That should be especially bad in a huge arena compared to smaller arenas.
Limiting side switching flattens out those fluctuations, at least in theory.