First, magically active characters (and technomancers) have to be very cautious about how they spend their Karma. There are many scenarios where it would look like you would get a 'Karma refund' but you don't. For example, if you buy up your Magic from 4 to 5, costing 25 karma and then get your first implant, it drops your Magic back to 4 from the Essence lost. However, if you get your first implant before buying your Magic, your Magic drops from 4 to 3 and you buy it back to 4 for 20 Karma. 5 Karma difference, all based on the order you do things. The same is true for initiating before or after you join a group.
Second, because of this sense of caution, I would not let adepts rearrange powers after a certain point early in the game. If a new player isn't sure of what powers to get and finds out later that other powers would be better, that's fine, but once a player is comfortable with what they are playing, then it stays.
To balance this, though, I do use an optional rule from SR3 that allows an adept to purchase new powers at Power Point Cost x 20 Karma, but unless he is upgrading an existing power, he needs to find someone that already has it to teach him. Brand new powers are always available when raising their Magic (thus how new powers are first discovered).