It is harmful to your eyes even if you feel so good to scratch your eyes in the morning. You may get the invisible bacterium into the eyes through the surface of the eye skin which may let your eyes get infection. Then your eyes may become red and feel itchy. You'd better not do this any more.
Yes, scratching our eyes really feels good, and also we want to scratch our eyes many time a day, for example, when we feel our eyes are dry or tired, we cannot help scratching our eyes. Maybe you do not know, our body are continuous producing hystimines which are a natural chemical anesthesia, at the same time, when we are scratching our eyes, the scratching are releasing the hystimines. On the other hand, if you feel your eyes are itchy, your scratch your eyes just to get rid of the annoying itches. Nevertheless, the scratching can help you with many problems, as you said scratching more will harm your eyes, such as the pink eyes or eye infection. As a matter of the fact, you can scratch your eyes when needed, but you should know that the scratching must not last long because scratching also have some side effects to our eyes. :)