Lynette,
Yes, you can control the color using an ArcReader template. ".art" file.
In your install location Desktop<>/bin folder there is an ARConfig.exe
You can use it to create a .art file.
It has a lot of setting, but on the Hyperlink tab you can choose the symbol that you want ArcReader to use for displaying the hyperlink highlight.
Then when you publish the map in Publisher Setttings load the .art file you created. This information will be included in the PMF and ArcReader will display the hyperlink with the chosen symbol.
mark