Skills and wizards, in part, says
The ability that controls bonus spells depends on what type of wizard your character is: intelligence for wizards; Wisdom for clergymen, druids, paladins and rangers; or charisma for magicians and bards. A caster must not only have a high skill rating, but must also have a sufficient class level to cast spells at a particular spell level.For example, the sorceress Mialee has an intelligence score of 15, so she is smart enough to get a first level bonus spell and a second level bonus spell. (She only gets the 2nd level spell when she is 3rd level wizard, since this is the minimum level a wizard needs to be able to cast 2nd level spells.) (Player's Handbook 7-8 and emphasis from me)
Despite the performance Early apprentice grant the creature "an additional 2nd level spell slot that must be used initially to cast only the chosen spell" (Complete Arcane 181) As shown above, until the creature's class levels in its Arcane Spell classes allow the creature to cast 2nd level spells, the creature will not receive 2nd level bonus spells due to a high skill rating.