Regioselectivity of an amination reaction of 2,6-dichloro-3-nitropyridine
I'd agree that nucleophilic substitution at C-6, leaving the nitro and piperazine substituents para to each other, would lead to the thermodynamic product.

The observed regioselectivity is therefore probably kinetically controlled. Although the nitro group activates both ortho (C-2) and para (C-6) positions towards nucleophilic substitution via resonance, it's worth bearing in mind that the nitro group is also extremely electron-withdrawing via the inductive effect in its own right.

This would make C-2 more electron-deficient and hence prone to nucleophilic attack.

Recall that in an SNAr reaction the nucleophile must attack the π* orbitals of the arene, which are above and below the plane of the ring. In this case, the nitro substituent is also (for the most part) in the plane of the ring, and doesn't lie along the trajectory of nucleophilic attack. So, the nitro substituent doesn't present all that much steric hindrance to the nucleophile.