I think so, Deaton is strange about Stiles, too strange for it to be a human thing. Stiles knows about the supernatural but he’s also uncannily intuitive and very good at research. He figures out a lot about the Hale Fire with half the information his dad does and feeds it to his dad. Stiles figured out the Kate thing without a lot of the information.
There are things about Stiles that are strange in retrospect, more than human if not necessarily supernatural but Deaton should have no reason to exclude Stiles. Recruiting Stiles would work better for him if he had nothing to hide, but yet we see him push Stiles away, it’s a surprise to learn that Deaton was working with Scott, that Scott stopped listening to Stiles plan’s and instead went for Deaton’s, which we see by 212, and even in 3a going with Deucalion suited Deaton not Stiles, Stiles tried to come up with an alternative.
Stiles also is moving more and more towards Derek because Deaton is pushing him away, there is a lot of evidence that Stiles helped Derek over the summer look for Erica and Boyd, but Scott knew nothing. Why wouldn’t Scott, in his training to be a true alpha (something Deaton never mentioned to him btw) not be out looking for pack.
Why would a lowly beta meet with the alpha pack if not to betray his alpha unless it was arranged by their emissaries. We know Deaton and Morell have history. How else was that set up? and there was only one way that meeting was going to end - both Deucalion and Deaton knew it - with Derek showing up. Both counted on it. I do think that scene was a trap but I don’t think Scott knew it was a trap.
With Derek out of the way it would be much easier to make Scott an alpha but yet Stiles in that episode as Scott was overcome with wolfsbane didn’t seem to think Derek was dead, neither did Boyd or Isaac. They both just shrugged Scott off when he said it and they would have felt it.
Deaton doesn’t like Stiles and Stiles doesn’t really trust Deaton, he sparks his evil-dar, he trusts him because Scott trusts him but notice he called himself Scott’s yoda but he called Deaton his obi wan, and made a big deal of the fact scott hadn’t seen it - meaning scott didn’t know that obi wan’s zealotry betrayed anakin and caused him to fall.