I think that Silas is telling the truth about Qetsia I think she really was obsessed with him becase it fits and explains a lot I mean why not just kill him why go to the lengths she's gone to? Also if she was played why would she take it out on innocent supernaturals by trapping them in The Other Side? Her actions match those of a vindictive possesive prideful psychotic woman.
Besides we all know the witches are sometimes nuts being opressed by the spirits I suspect Qetsia has on the other side gone mad with power and is now like Hitler or Stalin. Think about it the Other Side isn't natural it wasn't created by nature and is itself an abomination which is probably part of the reason Silas might want to destroy it. Qetsia is probably using her own religion or created one to justify her actions and influence future generations of witches.
If nature was really at the core of everything then what about voodoo, expression, and dark magic? When you think about it the spirits actions contradict what they say they are about and Qetsia's obsession explains that. Silas might not be a good guy but he might be trying to fix things but going about it the wrong way.
Also Silas may not be a witch but I suspect he might be a different species of vampire.