The city had completely shut down, the Petrograd society was unaware that Tikhon was here, and far too distracted to be looking for him

I'd turn the first comma into a period and add a "was" before "far too distracted", though this seems like my stylistic choice more than anything.

It was working, but working too well, the chaos had far outstripped what the Moscow wizards had ever intended.

Second period could be a period or a semicolon or a dash. Depending on your tastes.

and she was pouring kerosene on it with intent in order to burn down a city.

"With intent in order to"? Sounds like a conflation of "with the intent of" and "in order to"

This is madness, witch, if you continue to feed this working then no one, not even you, will be able to control it

Unless it's a deliberate stylistic dialogue choice, I'd change to "This is madness, witch. If you continue to feed this working, then no one - not even you - will be able to control it." The dashes could be commas if you feel it fits the style better.

Use it to destroy your enemies, with my blessing Tikhon.

"destroy your enemies with my blessing, Tikhon" ? I think that slightly changes the meaning of your sentence, though.

"It's for your own good, boy," the woman said, "some things aren't meant to be seen as they are, even for wizards."

The comma after "said" could be a period, and "some" will then have to be capitalised.

That's the last of pedantic punctuation changes. :p Great worldbuilding here that definitely reads like it needs a sequel.