Your post is still relevant after 4 years. Did you find a solution meanwhile?
We've experienced the same problem on 28 workstations whith Adobe InDesign CC2014/2015.
With Balance Columns turned on it's nearly impossible to work productive because you spend more time with waiting than working.
Even a simple text correction like adding a comma takes several seconds latency. It's just unsuitbale to work like this.
Yes I found a solution, and it was to not work that way and work a different way.
If you can find another way to do your layout without it crawling I suggest you use it.
Disappointing after 4 years there has been no resolve to this - but hey we can now instantly publish something online, or shade a paragraph, etc... but real matters are not being addressed.
We're facing the same problem here.
When using the feature "balance colums" performance of InDesign is going down that working is nearly impossible.
We tested several things to track down the problem, but it really looks like a bug.
It's ridicolous that it persists for such long years and even appears in the latest version of InDesign CC 2015.
I opened a support-case (ID 186875299) at the Adobe Enterprise support. Let's hope they will seroiusly look for that case to find a solution.