Create a paragraph style which has the default settings of your body copy (black) and apply it to all the text.
Create a character style which only applies Character Color: red. Character styles are different than paragraph styles because they only apply the specific attribute(s) you give to them. Apply the character style to the highlighted keywords.
If you have a limited number of words to which you want to apply the red, you can add them to a GREP style nested in the paragraph style to automatically add the red character style. Otherwise, best bet is a variation of the Find/Change by List script to find all your words, but you'd have to re-run the script each time you edit.
If you want to add the styles to an already created document:
1) Create you Character style containing only the character color
2) Find and Replace, searching for text with red color and replace formatting with the new character style. (Don't type anything in the text part of the Find and Replace dialog)
3) Create and apply your paragraph style to all. The text with the Character Style applied will stay red.