I think I misunderstood your question at the beginning, and after re-reading, I think I get it.
You're concerned because you feel that you should have been able to negotiate a harder deal, because the appraisal came in only slightly higher than what the two of you agreed on.
It's very common, in today's market, for appraisals to come in at EXACTLY the purchase price. Appraisers are hesitant about "over-appraising" property, and to that end, often match the purchase price, if they find that they have documentation that can support it. It's very common to find appraisals coming in BELOW the agreed-upon price, and then the buyer and seller find themselves @ "decision-time" trying to determine if they go forward at all, or renegotiate the contract.
So, I think you did well... you drove a hard enough bargain, that the appraisers felt comfortable appraising your property HIGHER than the agreed upon price... you may still feel free to do that dance. You rock!