Greetings,
I agree those scratches look horrible, but they are superficial and will not affect cooling performance. Options now - I'd put it back together.
For future: Any modifications, thermal paste, etc can be grounds for a denied warranty claim, once you start taking stuff apart. I'm not suggesting you did anything, but taking the cooler off a new card without even testing it... that's looking for trouble. If you do have a future problem.. A vendor could ask you what you were doing in there in the first place... or if their was a performance problem to begin with?
Not much else to do now, but put it back together.
