A few points:
i) you don't actually need to jump directly to second order logic in to get a categorical axiomatization of the natural numbers. There are several weaker ways to do the job: L_omega_omega (which allows infinitary conjunctions), adding a primitive finiteness operator, adding a primitive ancestral operator, allowing the omega rule (i.e. from the infinitely many premises P(0), P(1), ... P(n), ... infer AnP(n)). Second order logic is more powerful than these in that it gives a quasi categorical axiomatization of the universe of sets (i.e. of any two models of ZFC_2, they are either isomorphic or one is isomorphic to an initial segment of the other).
ii) although there is a minority view to the contrary, it's typically thought that going second order doesn't help with determinateness worries (i.e. roughly what you are talking about with regard to "pinning down" the natural numbers). The point here is that going second order only works if you interpret the second order quantifiers "fully", i.e. as ranging over the whole power set of the domain rather than some proper subset of it. But the problem is: how can we rule out non-full interpretations of the quantifiers? This seems like just the same sort of problem as ruling out non-standard models of arithmetic ("the same sort", not the same, because for the reasons mentioned in (i) it is actually more stringent of a condition.) The point is if you for some reason doubt that we have a categorical grasp of the natural numbers, you are certainly not going to grant that we can enforce a full interpretation of the second order quantifiers. And although it seems intuitively obvious that we have a categorical grasp of the natural numbers, careful consideration of the first incompleteness theorem shows that this is by no means clear.
iii) Given that categoricity results are only up to isomorphism, I don't see how they help you pin down talk of the natural numbers themselves (as opposed to any old omega_sequence). At best, they help you pin down the structure of the natural numbers, but taking this insight into account is easier said than done.