Well, if you look at UIBarItem (the superclass), there is a UIImage property. If you look at UIImage you will see a "+ (UIImage *)animatedImageWithImages:(NSArray *)images duration:(NSTimeInterval)duration" property.
Thus, I assume (but did not test) that you can create a series of images that when sequenced through will do what you want.
Alternately, you can subclass UIBarButtonItem, and provide your own "setTag:" method so as to intercept that message, and use special values to signal that you want pulsing on and or other states.
That method would get the image properly, the CGImageRef backing it, fiddle with it (color, opacity, whatever), then do a super.image = modified image. Have no idea if this will in fact work but at least may give you some ideas.