Use a script to add vertical justification only where there is vertical spacing (you can do an 800 pg. book in a single night by hand if you need to --- ask me how I know that and I'll cry into a beer). If you also only use paragraph and character styles you can remove it and redo it from a particular section of text by selecting it, right-clicking and "clearing over-rides". For multi-column work you'll also want scripts to break multi-column text frames into sets of single column ones and stitch them back together. Let me know if you want them.
The annoying thing of course, is there was a nifty free plug-in for properly doing vertical justification in Quark Xpress.
Or, of course, one could just use TeX, which is what I'm glad to've pretty much gone back to.
William