Generally "it's the thought that counts" is used in the context of gift giving, when maybe the gift isn't what one 'expected' or 'wanted'. Lets say, one of your friends gives you a framed picture of 12 year-old you for your birthday. It's not the most flattering thing ever, but hey, it's the thought that counts. The sentiment is more important than the physical. In the context you're in, it's fine to say something similar to that :) "Thanks, but you really don't have to do that. I do appreciate the sentiment, though." This will depend on how close you are to the person, however.