I'd say he's establishing an aspect of his faith in magic and compelling the high-concept of the vampires to keep them at bay.

Pretty much.  I'd call it a power instead of a stunt.  But seeing as you have to have a power as a prereq anyway, the difference between a stunt and a 1 refresh power is academic.  I think the homebrew power people around here often use is Alternate Magical Paradigm.  I think that's a touch too powerful, myself, but not so much as to disallow it.  If you just want to use it as a stunt, changing a single trapping of a skill (like an implicit controlling casting trapping) is the first example of the proper power level of a stunt, so your stated stunt is a little weak (since it's one trapping conditionally), but still functional.

This Word of Jim pretty thoroughly implies that Baba Yaga is Mother Winter.  Or Mother Winter is Baba Yaga.

I finally got around to reading the story.  It's a good read.

Penny seemed to have a plenty large role, even from the start.  She was suitably naive.  And heck, she even survived.

Katya was every bit as dangerous as she was intended to be.  When she is in a fight nobody actually ever sees her.  She even gets a little conversation time in the story.  There was one way that Katya in your story differs greatly from the Katya I wrote, and that is she allowed a Lawbreaker to live.  My Katya would not do that without some very serious mind control going on since her high concept was Greycloaked Assassin of Warlocks.  That said, your Katya fit the story and provided the quite significant level of opposition your protagonist needed.  So overall, I'd have to say she was well used.

The character absolutely should have an aspect about the item of power.  But I agree that Bearer of Bjornedyr is a bit boring.  Think about how he feels about the item and what it represents to him.  That should lead you to what sort of invokes and compels you want and that should help form your aspect.  Here are some examples.

Honored by Odin with Bjornedyr - If the character likes Odin and getting the axe was the greatest moment of his life.  Invoke to be in Odin's favor, compel to have the character need to stay in Odin's good graces.
Exit Through the Bear Door - If the character uses the axe to escape from situations.  Invoke to be able to leave a situation, compel to force you to leave via the nevernever even if it isn't necessary.
An Axe so sharp it can cut Reality - If the character takes a more secular view of the axe.  Invoke to chop things, compel to have the axe accidentally cut something.
The Onus of Bjornedyr's use - If the character sees the axe as a responsibility.  Invoke to stay true to Bjornedyr's purpose, compel to have the character take responsibility for more things (like things that escape to/from the nevernever through the holes that he cuts or for actions of previous bearers of the axe)
I wrestled a bear in the nevernever and all I got was this lousy axe - If the character isn't exactly grateful for the axe.  Invoke on Wrestling, compel for the character to express ingratitude.

Now I kinda want to use that last one.  I went into a frenzy in Norway and all I got was this lousy shirt or something like that for someone who became a berserker (literally bear shirt).

I've got about three wizards that I've used that might turn into a good story.
Penny is young, exuberant, naive, kind, and in over her head.  She is a decent thaumaturgist, but still hasn't developed her evocation skills, and has impetuously made a deal with the Summer Court for summer magic to supplement.
Livia is carefree, larcenous, curious, nonviolent, and incautious.  Her magic is most influenced by her First time is the charm aspect, which means she can usually whip up an improvised spell to bail her out of the bad situations she keeps getting herself into, but can't necessarily do it again when she tries.
Katya is experienced, paranoid, precise, patient and unflinching.  She relies on her thaumaturgy most, doing crafting, conjuration and veils with expertise, all things that reflect her character.

It's a little bit of a cop-out , but you could say that the Ghost in the Machine is too alien and too enigmatic and too intelligent (and yet at the same time probably incredibly naive) to be understood by humans and model the agenda with randomness.  Just roll a fate die and if it comes up a "-" then the Ghost does not approve of that course of action.  Bonus points if you don't let your players know you're doing it randomly and they constantly try to figure out what the agenda is.

The alternative is to figure out the story behind the Ghost in the Machine.  Maybe it was a digitized human mind that got trapped there.  Or maybe this guy's ghost got stuck in the first computers and has grown and adapted to his new home and all he wants to do is feed on flowers and fly towards lights, neither of which exist in the machine world.  Alternatively, the Ghost in the Machine might have a less biological origin.  It might be the last lingering fragment of Hephaestus.  Or it could be an accumulation of all the emotions: hopes, fears, lusts, and angsts that humans have poured into the internet in its short history.  Or it could be an entity made by Mother Winter to subtly enhance humanity's cruelty.  Just pick an explanation then figure out what that means for the agenda.

One of the PCs is a Hydromancer, my worry is that he'll cotton on to a circle of flowing water to both trap him and ground/isolate his magic. I don't want to be caught flat footed by this so ... .... Any ideas how the Sorcerer Blampire would get out of that one?

I would say that the PCs shouldn't be able to trap him because they shouldn't be able to find him.  Have him assault the PCs with endless waves of baby BCVs and renfields and thralls, just trying to do a little damage to them.  Then they come in and scoop up the hair or blood and deliver it back to their master for whatever nasty ritual he has planned.

If you want him to have a plan beyond that... maybe his final lair is in a salt mine where the only water is the stuff you bring with you.  No moisture survives the dessication of the salt.  There are some in Detroit, Louisiana, and Virginia.  Or maybe he is hanging out in a graveyard and if the PCs circle him he has a lackey call the cops and say that the PCs are a grave-robbing ring and when the cops show up he just holds still.  Or maybe he just has sponges or sandbags to throw in the way of the water before the circle can form.  Or maybe he's just out in the middle of a desert if you want less sophisticated dryness.

Although back on the does magically manipulated running water count topic, I wonder how much water magic can actually manipulate water.  The strongest example of water magic is Carlos's green beam, and that isn't actually manipulating water at all, it's manipulating a concept (entropy) that is related to water.  Dresden manipulates water much more directly than that with his ice tricks, but that used fire magic.  Can anyone think of any official examples of water magic actually manipulating water?