Two things to keep in mind:
First, Cloak of Shadows is not Cloak of Invisibility. It makes it easier to hide in the shadows, but does not grant the ability to hide in plain side.
Any source of light will cut through the shadow with ease. The cloak does not create shadows, it uses them. Infrared detectors don't rely on visible light, shadows don't affect them. The same goes for magical detection, for example a web spell like Harry does in PG. There are a lot of things that can make life for a sneaky character complicated.
Second, if the Character has Cloak of Shadows, sneaking around is what he does. There is no reason why he shouldn't be good at it.
However, you don't always have to make a stealth vs. alertness roll and be done. You could also, for example, turn it around, if your character wants to get in somewhere. Give the target a security rating, like an alertness skill, and then add on a few aspects, each adding +2 to the rating. You can add fairly simple things. Good lighting, guard dogs, cameras, well drilled security personal, and so forth. Now your thief has to get around those things, either by creating aspects and adding them to his own roll, or by countering the security aspects.
Another way to make life harder for him would be to have him take someone with him. Sneaking in and out of places is a lot more difficult if one of you has no clue what he is doing. Or the other one doesn't fit through some of the narrow passages the thief is used to going through, so he has to work around them.
I'm curious, how exactly did your player abuse CoS? Can you give an example? Maybe there is an easy workaround.
