Do you think that Source skills should count for that deliberate exemption?
Short: Yes.
Long: Attaching another form of cost to the skill constitutes valid grounds not just for a deliberate exemption, but for a different evaluation scheme in general.
Also, the effectiveness of the current or any new system would need to be assessed for character levels higher than we will get in the Early Release game.
Adding granularity(such as by making Memory operate on a 1:1 basis for 'slots' added, and then increasing the costs of skills to be generally double the current), doesn't really run into any immediate balance problems.
The only special consideration it requires is to ensure that there exist odd(1,3,5, etc.) number cost skills to allow the player to take advantage of an odd number of Memory.