The difference is that scientists in the past never used "god did it" as a scientific explaination. Once you say God did it you cannot look any further.
For example Intelligent Design claims the bacterial flagellum is IC and therefore must be intelligently designed. However anyone who believes this conclusion would immeditately stop looking for natural origins for the bacterial flagellum. That is pulling the plug on this line of research.
So what do they do instead? Well they just don't.
ID people admit they can't study the design process, or anything about the purpose of the object, or anything about the designer. So once you conclude an object is intelligently designed there is no more research to be done on it's origin. You simply move on to the next object.
So it really seems to me that claiming an object is ID is effectively a research stopper.
That is not true but I have heard it a lot. In fact many evolutionists claim to believe just that. They say the Bible says who did it (God), but it doesn't say how he did it (evolution). That is precisely "God did it and then looking further after accepting that God did it.
So it can be said quite logically that you are wrong in your statement that people cannot say God did it or they end science right there.
On the contrary, you can say God did it and then take it apart and look at it your whole life and see how it works and how He may have done it.