Out of curiosity, how do you deal with the 'I have a Weapon 8 "THROW OBJECT" Rote! I use telekinesis to throw cars at the enemy - cars aren't magic!'
This seems to be the default for Wizard PCs to get around magic immune monsters.
I allowed it, because:
A: By the time they've figured out the monster is immune, they've already used up at least one spell and probably taken a pretty solid hit from that monster;
B: The monsters who were immune to magic (like ogres, grendelkin and one Black Court Elder who had done her homework on the PCs)
also tended to have some other toughness power, so that Weapon:8 tree they get hit with is still unlikely to be a one-hit-kill.
C: It's creative property damage and if they're actually making use of their environment, that should be rewarded with success.
Tailoring your antagonists to your PCs is a good idea, too -- one of the PC wizards had the aspect "Terrifying Reputation," which is why that Black Court Elder didn't come to the city without making herself immune to magic.
Said PC wizard also had a tendency toward fire magic, so when there were assassination attempts on all the PCs, the villains sent a fireproof dragon at her.
The other PC wizard at the time was blind and only saw auras -- so a mortal gunman was able to get in close and land a few gunshots on her before she knew what was up.
Or, slap them in thorned manacles. I did that to one wizard PC in the first scenario and tossed her and the mortal cop into a boss fight against an ogre and a wizard. The still-bound wizard PC was able to get the villainous wizard in a stranglehold and all but incapacitate him with the manacles.
There are tons of ways to neutralize a PC wizard while still letting them participate, so long as you're willing to shell out some fate points and compels.