It seems that iTerm2 is hardcoded to highlight search results using a yellow background color. I tried both the latest release and the nightlies but could not find a way to change that color.
Did I miss something? It seems implausible to me, that a terminal emulator with such a degree of customizability would really hardcode a single color while at the same time making virtually everything else user-configurable.
For clarification, here's a screenshot: As you can see, I searched the screen contents for the word "stack" and all its occurrences are highlighted in yellow (except for the selected one).