The issue in 3.5 is that (Wizard and Sorcerer, and certain other) arcane characters automatically qualify for a familiar, regardless of character concept.
If they aren't interested in roleplaying out what amounts to an additional NPC (and the DM doesn't want to either), that's kind of a problem. Although players usually don't balk at the idea of the little benefits they get from the familiar when they come up.
At low levels, the 3.5 Familiar generally grants benefits equal to a feat: A skill focus feat, toughness (for the toad), etc. PLus the Alertness feat.
One idea is that you just take the equivalent bonus of the familiar and attach it to something Non-animate (thus removing the NPC qualities of it)- for example- a tattoo or a personal Hex/charm/totem.. that the wizard might have-- that grants the exact same benefits of the Familiar.
A Wizards Tome or grimoire could be the focus of such a benefit- as long as she carries the grimoire, she gains the equivalent of a Skill focus feat (chosen at the beginning of a campaign). To account for the loss of Alertness, you might say that the Skill focus feat is reconfigurable between adventures- these are magical books, after all, able to grant advice on any manner of subjects.
Whatever you choose- I recommend that you don't go far beyond the established structure of a feat (possibly with or without alertness) as the benefit.