Like the others said, adjustments on the fly go a big way.
On balancing magicians/magic, that's a bit tricky. I wouldn't try to compare what a mage can do vs what a mundane can do. That's the uncool way to balance things. Instead, mages have incredible power at their fingertips but more consequences for it's use often times.
Often times a combat spell's damage is compared to a Sam's gun's. A Sam can get bigger and bigger guns too if they like, the problem with that becomes money and concealment. A mage seems unbalanced because they can output that same crazy damage without having to buy anything new and conceal-ability isn't an issue... Or is it? Every spell, focus, spirit leaves an Astral Signature that can be tracked back to the mage, every spell can be observed as it is cast by the noticing magic rules.
Anyhow, my point is that a great deal of balancing magic is not using the rules so much as using the setting and the rules together. Magic is rare, so it's memorable - witnesses will be more likely to remember a mage's face, clothes, etc, if they've observed him/her making magic or saw a spirit. Any law enforcement agency worth a damn will bring in a mage of their own to check for astral signatures if they believe magic was involved in whatever they're looking into, records will be kept, etc. My own game I tend to make things of a magical nature drawn to or at least take notice of other powerful magical occurrences, so toxic spirits might show up and take interest, etc.
A mage is totally unbalanced in terms of a fight alone. But looking at the bigger picture, they have a lot more ways to be tracked down. The normal things like DNA evidence (blood from being shot, etc), fingerprints, being caught on camera, all that just like anyone else, but also a whole bunch of things that other characters don't need to worry about. If a GM neglects these tools, then mages are likely to use as much power as they can. But if the players know that there are consequences for becoming a "walking talking magic death machine" then they'll have their character play it safer and use more reasonable amounts of power.
Do this and the player will balance their own character by keeping themselves in line, for the same reason a Sam doesn't use a panther assault cannon for every encounter. They could, but they know they'll get into bigger trouble for it. If your game is more pink mohawk and doesn't bother with tracking down players too much, then use background counts to your advantage. Just a general city area should be a -1BC due to pollution and such if I recall correctly.
