Going from the topological index idea: let $C$ be a circle around one of the isolated zeros, and let $D$ be a disk containing $C$. By the trace theorem, your vector fields in $W^{1,2}(D)$ restricts to vector fields $W^{1/2,2}(C)$ on the circle. Since they do not vanish, you can regard them as vector fields $W^{1/2,2}(C, \mathbb{S}^1)$. (If there's any problem with my argument, it would be this step, passing from an $\mathbb{R}^2$ valued function to $\mathbb{S}^1$ valued one.)
The $W^{1/2,2}(C,\mathbb{S}^1)$ functions are continuously embedded in $VMO(C,\mathbb{S}^1)$ since $C$ is one dimensional, and one can use the $VMO$-degree theory (originally due to Boutet de Monvel and Gabber, and extended by Brezis and Nirenberg, see this survey by Brezis). The upshot is that for continuous functions the VMO degree coincides with the the usual topological degree, and the $VMO$-degree is continuous under $VMO$-convergence. So I think Pietro's argument against the $W^{2,2}$ case using degree theory should carry over also, telling you that you shouldn't be able to do your approximation.
To be more precise: the chain of arguments should go something like: since your $V_n$ are in $C^\infty$ and has no zeros, their corresponding topological degree would be zero, measured either in $VMO$ or classically; but $V_n$ converges to $V$ in $VMO$ (by argument above), and this means that $V$ has to also have degree zero, a contradiction.