Why would you want to turn a Fighter, of all things, into a ninja? That's crazy talk! A samurai Fighter (or Paladin), on the other hand, would be quite workable.
Combat and skills are not mutually exclusive. Ambushes rely on stealth, Tumble helps with mobility, etc.
If you want to make a ninja character without using any "oriental"-flavored material, I don't really see how it requires any more than playing a Rogue and having your Rogue wear a black jumpsuit and, um, one of those... black... hat-mask... things.
The actual Ninja class from Complete Adventurer is basically a cross between Rogue and Monk.
I dunno, I think that something more like Arcane Trickster or Psychic Rogue would work better for a magic!ninja.