Sorry i have updated my unity to the new UI 4.6 so i don't remember exactly how to do it but you should first get the Gui text component then acces the color alpha.
var GuiLabel : GUIText;
GuiLabel.color.a = yourValue;
//OR
SomeGameObject.GetComponent(GUIText).color.a = yourValue;
If you are getting an error post it and post your code.
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