I too originally read it as saying that it was expected to be bad coming from Amazon. And the "in my defense" part is that, if you know the coder is from Amazon, then you understand why the code might actually be truly bad enough to elicit a chuckle (as opposed to just chuckling at normal bad code). In other words, it's like saying "in my defense, it was super bad code".

That said, I think the interpretation that "he had 3 years experience at a big company, he should have been better" is probably the correct one.