"Quick reply": does it mean responding in a timely manner or something like 'your answer was super fast you could've put more thought into it'?
Because if you say "thanks for the quick reply" I think it's the first but if you write "here's a quick reply" I think it's something you've put together in a rush, maybe because you're about to go out and you'll elaborate later.
Best Answer
I look at "thanks for the quick reply" without context and it does seem as though it could have sarcastic intent to me. However, I think this could be corrected by simply changing the informality of the "thanks" for a more formal "thank you"... although if you are still uncomfortable you might use the words "speedy" or "prompt".
I'm sorry, but I think that this is largely a matter of context which could hold an almost infinite amount of sway over the final meaning of the phrase.