I wouldn't be so quick to say you're conditioning the snake to be aggressive out of the tank if you feed her in a separate enclosure. Because conversely, if you fed her in the tank, she would become aggressive when you'd go to pick her up, because a hand in the tank would mean food.
If the ONLY thing you were doing when taking her out of the tank is feeding, then yes, you'd be slowly conditioning her to be aggressive. Same case with feeding in the tank. But because you're doing different things when taking her out, like handling her and letting her roam around, she isn't being conditioned.
I'd be willing to agree that it's simply a grumpy, stressed out snake.
You're more than welcome to try feeding her in the tank, as I don't think either method (in-tank or separate enclosure) has any real impact on aggressive behaviour, but I would definitely handle her a little less.
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