If you run an InCopy workflow, or you have found this post by searching the web, you probably know the issue with markup up index words in InCopy - the tool is missing.
In the projects where we run an InCopy workflow, it is mainly books, where the editors easily can proofread and correct in the story itself, and letting them mark up index words would be a great in that process as well. I can't see any obvious reason to why Adobe left it out, other than InCopy might be more minded on magazine editing(?), and there isn't much use for indexing in magazines.
The solution
In books where the index are marked up late in the process, after the book is typeset and proofread, we either mark it up ourselves from a printed copy with highlighted words, or we let the editors mark up the index words in InCopy using a colour swatch. When we receive the InCopy story from them, an AppleScriptJavaScript in InDesign takes care of finding all the coloured words and marking them up as index words. When the script is done, a quick search/replace takes care of colouring the words back to their original colour.
The dialog box that asks you which swatch you want to make an index from.
The script might come in handy in other cases as well, but the InCopy case is the most obvious. The same script could be done with character styles as well, but since I'd like to enable marking up that already have a character style applied, I found swatches better suited.
The script
I have uploaded the basic script - letting you select a swatch from a list and it searches the current document, marking up words. You are free to modify it to your needs - might come in handy to convert words to lowercase or things like that.
You can add it to your Scripts palette and run it from there. To do that, place the file inside the "~/Library/Preferences/Adobe InDesign/Version X.0/Scripts/Scripts Panel" folder.