Unless Kubo is doing some sort of meta-mindfuck where he makes us think Urahara is evil but then doesn't actually have him be evil, then yeah, he's evil. And I don't think it would create any problems. The guy's been mysterious and manipulative since his first appearance.
In the current arc he's been revealed as the warden for prisoners held without charge (and perfectly fine with it), willing to let psychos out of prison, and probably the one behind all the mass murders, since the souls vanishing are being turned into hollows and Aizen, the only other option, never experimented on shinigami, only hollows.
Add on that he almost certainly gave Ichigo an inner hollow intentionally, possibly set up the hollow that attacked Rukia in chapter 1 (tankobon edition has him at the scene literally seconds after the end of the fight).
As for Aizen, the guy seems to be being presented more and more sympathetically. A lot of people ignored it since The Great Pumpkin was the one to say it, but arrancar aren't necessarily evil, while Soul Society simply doesn't care. Aizen has in a sense been leading their race towards the light ever since he first started experimenting on raising hollow intelligence levels.
Sure, Aizen still has a few unnecessary murders on his record, but Bleach seemed to stop caring about little piddly details like that back when it decided to give the protagonist powers fueled by hatred for all sentient life.