The main difference between $\mathbf{F} = -\nabla U(\mathbf{r})$, which is true for a conservative force derived from a potential $U(\mathbf{r})$, and the proposed equation $\mathbf{a} = \dfrac{1}{2}\nabla(v^2)$, which is not true, derives from a subtle difference in how we should understand the functional dependence of $\mathbf{F}$ and $\mathbf{a}$ on $\mathbf{r}$ in each case.
The identification $dU = -\mathbf{F}\cdot d\mathbf{r}$ is true for any spatial displacement in the position $\mathbf{r}$ in any trajectory---after all, it is essentially the defining relation between force and potential energy in a conservative system. The step where you replaced $\mathbf{v}dt$ with $d\mathbf{r}$, on the other hand, is only valid once a trajectory has been fixed. This automatically means that any functional relation between $\mathbf{a}$ and $\mathbf{r}$ obtained after that step is only valid for one given trajectory, and is therefore no longer true if you treat $\mathbf{r}$ as an independent variable (as opposed to a collection of implicit functions of time, $\mathbf{r} = \mathbf{r}(t)$).
Just to illustrate how important this distinction is, let us assume for a minute that the answer to your question is affirmative, so that we can essentially treat $v^2$ as an independent function of $\mathbf{r}$ from which the acceleration is derived through $\mathbf{a} = \frac{1}{2}\nabla (v^2)$. By making use of $\mathbf{F} = m\mathbf{a} = -\nabla U$, we would get to
$$\nabla\left(\dfrac{1}{2}mv^2 + U(\mathbf{r})\right) = 0.$$
Now, at a superficial level, this may just look like the good old law for conservation of energy, $\dfrac{1}{2}mv^2 + U(\mathbf{r}) = \text{constant}$. But if this were true as a vector field in $\mathbb{R}^n$ (if space is $n$-dimensional), it would mean something much more restrictive than conservation of energy: it would actually imply that
$$\dfrac{1}{2}mv_1^2 + U(\mathbf{r}_1) =\text{constant}=\dfrac{1}{2}mv_2^2 + U(\mathbf{r}_2)$$
even for points $\mathbf{r}_1$ and $\mathbf{r}_2$ which are not connected by a solution to the equations of motion. In other words, not only would energy be conserved, but it would actually attain the same value (which we might as well set to zero by shifting the potential by a constant) among all solutions to the equations of motion. This is clearly not true in general, even for conservative systems. The version of the equation that is true is very similar to the previous one, but instead of having the gradient, we just have
$$\dfrac{d}{dt}\left(\dfrac{1}{2}mv^2 + U(\mathbf{r})\right) = 0$$
with $\mathbf{v}$ and $\mathbf{r}$ being treated as implicit functions of $t$.