I agree with this--I think Urahara looked guilty about more than just having unknowingly sent his vice-captain into some kind of bad situation; he looked like someone who'd unknowingly sent his vice-captain into a bad situation that he'd had something to do with causing.
That'd certainly explain why we've never seen Urahara and the Visored appearing to work together--if they have good reason to blame him for why they are the way they are now. On top of that, the Visored who all used to be high-ranking officers and not disgruntled proletarians from Rukongai (lol), and yet they all now hate shinigami, so this would imply that something about this secret project was being run by people within the Gotei 13, people whom some or all of them used to trust.
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That'd certainly explain why we've never seen Urahara and the Visored appearing to work together--if they have good reason to blame him for why they are the way they are now. On top of that, the Visored who all used to be high-ranking officers and not disgruntled proletarians from Rukongai (lol), and yet they all now hate shinigami, so this would imply that something about this secret project was being run by people within the Gotei 13, people whom some or all of them used to trust.