Don't forget counter magics!
If an invisibility spell seems to powerful, have any important areas guarded by 'see invisibity zones' that prevent it spoiling inapropriate parts. And have these security devices cheep and easy to attain. An experienced thief will know how to get past or disable them, and know what that rune on the doorstep does, etc.
You don't necersaryily need to totaly remove the offending spells, also because they're are also the ones that are most interesting for your setting. You just need to find a way to control their use.
teleport preventers (banks, rich nobles houses, prisons etc)
polymorph inhibitors
Invisibility jammers
sewer guards (the sewers would be an interesting thing to consider for your campain. gets you past the wall but have to fight the greasel)
Anti fly walls
dispell traps
Magic detectors
Other ideas could be a special division of the town watch specificaly trained to deal with such theives. Changeing the matierial component so that it has a small cost or is rare, so avoiding over casuall castings but not removeing it and making it so that you can easily regulate it. eg black market shop keeper - "I've only got three smoke opals to sell ya right now, hope ye not be needin invisibility too much?".
Make most of it defeatable in some way, so that they can always be one step ahead provided they do it right. And draw up a list of special gear and equipment, no master theive should be without her toys; 'The Theives Toy Box' was an instant favourite with my players, and I loved the way they gazed down the list going "ooh, that will be usefull" and "hehheh, can't wait to get one of those". Smoke bombs, magic rope arrows (a classic), flash rocks, slip sheen (for throwning down a slipery trap for pursuers), and spy arrows. All favorites.
Hope some of this is helpfull.