You make a good point, however Jesse is not stupid and by this point is generally distrustful of Walt having seen how manipulative and ruthless he is.
When he realizes that Huell lifted the cigarette from his pocket, coupled with the fact that Walt was present when the cigarette was "found" in Jesse's house, it makes him realize that it was a setup to manipulate him.
The tox screen finally indicating Lily of the Valley poisoning has little bearing on that conclusion - if anything it makes it more likely it was Walt's doing.
First of all the setup only required that Brock falls ill and that Jesse initially blames it on the Ricin cigarette. When the cigarette is found it means that the blame is elsewhere. It clearly wasn't Jesse's carelessness and the Ricin cigarette was in Jesse's possession all along.
A different poison to that actually used means its more difficult for Jesse to incriminate himself. Jesse would know that Walt would not want him to end up in too much trouble with the police.
Finally Jesse knows that Walt would only kill Brock as a last resort to protect himself - yes he's ruthless, but he's a father and not needlessly evil. Walt is more than capable of synthesizing a different less lethal poison for his needs.
Until the pickpocketing is discovered, Jesse is persuaded by Walt's argument that the poisoning was done at Gus's orders. Once he realizes that Huell did steal the cigarette, then the only conclusion he can draw is that it was all planned by Walt regardless of the poison used.