Sorry to necro this thread, but after extensive searching I couldn't find this, and this is the first thread that comes up.
Here's how to do it in Scientific Linux, and probably other flavors. First, Gedit stores its color themes as xml files, and clicking on Edit>Preferences>Font&Colors reveals the one you're using, let's call it MYTHEME. Running
find / -name MYTHEME.xml
as root in a terminal will reveal its location.
Copy the xml file to your home directory, rename it NEWNAME.xml, then open it and edit the hex colors in the line
<style background="#F8F8F0" foreground="#000000" name="cursor"/>
Now in Gedit under Edit > Preferences > Font&Colors you can add NEWNAME.xml and use it to get a different cursor color.