The official Pathfinder text states:
Coming back from the dead is an ordeal. The subject of the spell gains two permanent negative levels when it is raised, just as if it had been hit by an energy-draining creature. If the subject is 1st level, it takes 2 points of Constitution drain instead (if this would reduce its Con to 0 or less, it can't be raised). A character who died with spells prepared has a 50% chance of losing any given spell upon being raised. A spellcasting creature that doesn't prepare spells (such as a sorcerer) has a 50% chance of losing any given unused spell slot as if it had been used to cast a spell.
As you said, this specifies the consequences of using Raise Dead on any character with at least two levels that can be lost as well as those of first level, yet leaves Raising Dead on a second level character ambiguous. To my knowledge, there is no official statement specifying the consequences of raising a second level character; however, it stands to reason that because in either case, the punishment is two of some resource, that at the second level a character would suffer one permanent negative level in addition to one point of constitution drain. This is the conclusion that my own group, as well as several others I've seen do.