Well, if the Assassinate DC for Halflings is based on Rogue level, not character level, it makes the Halfling PrE something of a cruel joke. I mean, even more of a cruel joke than absurdly-low DC's already do.
Assassinate is already a marginal ability, given that it is only really usable if you're soloing or playing in a Permadeath guild. Few parties are willing to, or have the discipline to, give you the time to use stealth and make the approach without alerting the monster. If the ability is also unreliable when used, that number will drop from few parties to zero parties.
Per the original mock up of the racial PrE's in the let's talk thread it was stated character level.
EDIT with the QUOTE:
Originally Posted by MadFloyd
Each race will have an enhancement that adds another specific enhancement tree to the character’s available list of trees. Elves and Half-Elves, for instance, gain access to the Arcane Archer tree if they take the racial enhancement to unlock it. Dwarves gain access to Stalwart Defender. The player can choose to unlock the tree and then not use it, if they so desire. Trees unlocked in this way use the character’s total character level instead of class level for prerequisites and effects.