The reason being that throughout history there have been evil persons who belonged to good organization and they did not lose any of their power whereas in 3.5 they do.
They didn't have any power to lose. Real life clergy don't have magical powers to be rescinded by a disapproving deity, and I reckon you would be hard pressed to name a saint in any religion whose miracles were tarnished by corruption. (Not that I'm encouraging you to try, given forum rules pertaining to the discussion of religion.) In most settings, the divine powers of Clerics and Paladins are presumed to be actively granted to them by the gods, thus it only makes sense that the gods can rescind those powers as punishment.
Of course, Eberron's different because, as a deliberate design decision, they
wanted to have corrupt Clerics and it would not make sense for a corrupt Cleric to continue to hold office after his lack of power is revealed.
I'm a little more skeptical of alignment restrictions for other character classes. Neither battle rage nor artistic talent preclude a person from having a great respect for authority, tradition, and order. No amount of self-discipline prevents a person from believing in free will and individualism. And the idea that a protector of nature can be lawful
or good, but not lawful
and good does not make a damned bit of sense.
In my games, characters who get their powers from a god are required to abide by that god's ethos. This is less an alignment restriction and more a code of conduct, but gods whose alignment is more than incidental will have codes that enforce alignment guidelines.
Now depending on the setting this can be more or less unrealistic. The usual response is that gods walk the earth so they can monitor everyone and take away their powers but is the phenomenon of gods walking the earth itself realistic?
It's no less realistic than any other aspect of the campaign setting. The existence and activity of the gods are a part of the assumptions behind any campaign setting, and the rest of the setting is either consistent with those assumptions or it is inconsistent. It's all a matter of whether or not all of the assumptions of the setting make sense when viewed together.
The definition of Good or Evil is very broad and as you say it's not very clear but it must be thought in modern terms but with a world in black and white.
There's no reason that the morality of the campaign setting must be either modern or black-and-white. I certainly prefer games in which it is neither. I have a profound distaste for the modern view of morality that grows into outright repugnance when it compromises my enjoyment of heroic fantasy.