Ebisu did not say you cannot have more stamina than chakra.
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. He had too much stamina so he was dumping unnecessary amounts of chakra into technique. That's where chakra control comes into play. Now Itachi being Uchiha naturally inherits high levels of mental energy as the databook stated. His problem was his physical energy (yes) due to health.
But here's a quick run down just to recap the difference between stamina and chakra (which i'm sure you know the difference of).
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Now it is possible to have high level of chakra without having an extraordinary amount of stamina due to having powerful chakra. Having powerful amounts of chakra (uchihas) allow you to combined little amounts of energy to produce strong amount of chakra with only a little percentage. The only thing you cannot do is have both stamina and chakra gone which would leave you dead.
So Itachi does not have low chakra, he just have low amounts of physical energy (stamina) although his mental energy being Uchiha is higher than any other clan/shinobi that is not Uchiha. If you get into the whole shadow style jutsus like genjutsu, you'll know that it requires higher amounts of mental energy and low amounts of physical energy to use like a 7(mental) to 3(physical) ratio type of deal when converting energy into chakra. <-just an example.
Plus Itachi outlasted Hebi Sasuke in chakra