There's no method in the book for becoming a werewolf without it being an affliction. Since you've effectively gained 4 levels (ECL +2, and 2 extra hit dice) the GM should certainly be reluctant to just let you keep lycanthropy as an advantage.
If, as GM, I wished to allow a lycanthrope PC, I'd come up with a 'class' for it (as per Savage Species); in the case of werewolf I'd probably set it as follows:
Level 1: you now have control in human form, and need not make saves to avoid becoming evil. Your animal form remains a chaotic evil NPC; consider investing in chains or a cage. This will give your human form the following bonuses:
+2 natural AC
+2 wisdom
Lycanthropic Empathy (wolves)
Level 2: gain 1 HD of 'animal', which gives:
1d8 HP, +2 Fort Save, +2 Ref save, 2+Int Mod skill points.
Scent, +4 bonus to Survival rolls when tracking by scent.
Your animal form is still an NPC. You may acquire Control Shape if you wish, but have no control in animal form regardless, and may not take on hybrid form.
Level 3: gain +1 HD of 'animal'
1d8 HP, +1 Fort Save, +1 Ref safe, 2+Int Mod skill points.
You now can control yourself in animal form. You cannot take on hybrid form, however.
Level 4: gain access to hybrid form. Bonus feat: Iron Will.
Level 5 (optional): you are treated as a natural, rather than afflicted, werewolf. Lose any skill points spent on control shape; you may spend them on wolf class skills.
Note that in your first two levels you're an NPC when shifted; Atonement spells may be necessary if you accidentally do evil while in werewolf form.