We have a loan with a note amount of $1,002,000. However, the $2000 is a financed origination fee. Is there any way to argue that this should qualify as a small business loan? I don't think so, but it is located in a moderate tract, so I want to count it if I can (not a CD loan).

I agree with you, I don't think you could argue that it is a small loan to a business since the characteristic is "loan amount at origination" which in this case includes the $2,000 origination fee.