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It does look to have decent synergy. Not really MAD with 2 level dip, focus on DEX, then CHA, then CON. Be half-elf with skill focus (perception), everything else about the half-elf is good here, better than picking a different feat and an extra skill point. You'll still be the party scout even without Uncanny Dodge, made up for having +5 to perception. You'll max Stealth, Perception, Escape Artist, and Acrobatics as a scout. Since you'll have decent CHA, you should be the party face too and have a good UMD to justify doing this build. As a ninja, two-weapon fighting is the way to go. Weapon focus, weapon finesse, two-weapon fighting, and improved initiative are your top feats. Try to get weapon focus and weapon finesse through rogue talents. Consider two-weapon defense, toughness, iron will, defensive combat training, stealthy, skill focus (UMD), and piranha strike. You're going to have mithral breastplate asap, until your DEX gets to 24.
Ultimately, this is all about getting First into Battle's synergism with Ambush. And it is a good one, which will allow you to get into position quickly when surprised, almost every time. Therein is the mechanics problem, you shouldn't be surprised too often if you're doing your job as a scout! It comes at a bit of a cost. Smite Evil and the full BAB only helps to make up for the d6 sneak attack, skill points, rogue talent and ki point. The medium armor proficiency helps a little until you have enough DEX to get more out of a chain shirt.
I'd stick with 2 level dip into paladin at most. Channeling would do best with the Cities variant channeling and do little even then, one or two spells would be lackluster at best, divine health wouldn't be worth it, and divine bond makes you light up- not good for the sneaky. Stick with getting First Into Battle.
That aside, there is one real big glaring problem. Iomedae is the goddess of righteous valor, justice, and honor. Using poisons, sneak attacking, and other ninja-like activities just don't mix with those principles. You need Iomedae to be a Sword of Valor. If it were another deity, it could be argued that the dirty tactics are an effective way of destroying evil. But not with Iomedae. Get the GM to overlook this, and its still a modest synergy at best.