Maybe you can try a semi-permanent color or a demi-permanent?
As the others have already said about damage, the color may also come out different or wrong because of the highlights you already have...it'd be best to see a professional regarding anything about dying over highlights.
ETA: Certain brands of Demi-Permanent hair colors do not have harsh chemicals and are actually great at making the hair soft and shiny...my recent try with Redken Shades EQ was AMAZING...soft, shiny, rich (in color) hair...not harsh at all, none of that ammonia ish and is the #1 hair coloring gloss rated by stylists...Look around also for some other great brands and options! =D