Although this question has received plenty of (very good) answers, one thing that I feel has not been explained is that how exactly does Frobenius' theorem guarantee path independence of parallel transport.
I feel I can answer this now in a way I would have liked when I asked this question.
Let $\pi:E\rightarrow M$ be a smooth rank $k$ real vector bundle with a linear connection. Furthermore, let us assume the open region $U\subseteq M$ is small enough to be trivializable and also to admit fibred charts of the form $(x^\mu,u^a)$ where the $x^\mu$ are coordinates on the base, and the $u^a$ are linear coordinates on the typical fiber. Throughout this answer I will work solely in this open set $U$.
If $\psi:U\rightarrow E$ is a smooth local section, then it is parallel if and only if $d\psi^a+\omega^a{}_b\psi^b=0$ with $\psi^a$ being the local section's components in the fibred chart and $\omega^a{}_b$ are the matrix-valued local connection forms.
It is easy to see that the parallel transport is path independent if there exists "reasonably arbitrary" parallel sections, so the question is answered if a necessary and sufficient condition is given for the solvability of the above partial differential equation for the functions $\psi^a$.
Now, if $u\mapsto H_u$ is the horizontal distribution on $E$, it can be locally generated by the system of 1-forms $$ \delta u^a=du^a+\omega^a{}_b u^b $$ on the total space $E$, where the $\omega$ 1-forms depend only on the base points, and are in fact equivalent to the local connection forms in the sense of the isomorphism between differential forms on the base, and horizontal, projectable forms on the total space.
The horizontal distribution is given as the combined annihilators of this system. The local section $\psi$ may be seen as defining a non-vertical surface in $E$. It is parallel iff this surface is horizontal, eg. it is an integral submanifold of the distribution $H$. Therefore the partial differential equation above admits solutions iff the horizontal distribution admits integral submanifolds, eg. it is integrable in the Frobenius sense (indeed the original PDE is basically $\psi^\ast\delta u^a=0$).
Applying the local coframe criterion for Frobenius' theorem, the distribution is integrable iff the exterior derivatives of the defining system of 1-forms also annihilate the horizontal. The exterior derivatives are $$ d\delta u^a=d\omega^a{}_b u^b-\omega^a{}_b\wedge du^b, $$ but for horizontal vectors we have $du^b=-\omega^b{}_c u^c,$ so $$ d\delta u^a=d\omega^a{}_bu^b+\omega^a{}_b\wedge\omega^b{}_cu^c=(d\omega^a{}_b+\omega^a{}_c\wedge\omega^c{}_b)u^b=0,$$ where the last equality is understood horizontally, however since the form here is horizontal, this is a genuine equality. And for the "reasonably arbitrary" part to be true, this must vanish for all fiber points $u$, hence we obtain the usual $$0=d\omega+\omega\wedge\omega$$ condition.