Just came across this, which seems to be able to modify some of Xcode's behaviors by creating some sort of plugin. Maybe one can be developed to change text highlight color. http:/github.com/davekeck/Xcode-4-Fixins

Update:

I've finally managed to implement a Xcode "fixin" to do it.

You just need to open the project and build it. Doing so will install an Xcode plugin called "XCFixin_CustomizeWarningErrorHighlights.xcplugin" into ~/Library/Application Support/Developer/Shared/Xcode/Plug-ins. You can of course customize the colors to your liking.

Get the "fixin" here:

https://github.com/armadillu/Xcode-4-Fixins/tree/master/XCFixin_CustomizeWarningErrorHighlights