Here is an analytic proof not using differential forms. Restricted to $n=3$, it comes almost verbatim from Stewart, Calculus: Early Transcendentals.
To get started, let us naively assume that region $U$ is convex. The reason for us to make the seemingly too-much assumption is that we want to give a description of $U$ in terms of a single two sided inequality (in the form $a\leq x_i\leq b$) for each $i$. Let $D$ be the projection of $U$ onto the $x_1x_2\cdots\hat{x_i}\cdots x_n$ hyperplane (to avoid confusion, $\hat{}$ means the variable under it is absent). Due to the convexity of $U$, we can write $U=\{(x_1,\cdots,x_n)\in \mathbf{R}^n|(x_1,\cdots,\hat{x_i},\cdots,x_n)\in D\mbox{ and } f_1\leq x_i \leq f_2\}$ for some $\mathbf{R}^{n-1}\to \mathbf{R}$ functions $f_1(x_1,\cdots,\hat{x_i},\cdots,x_n)$ and $f_2(x_1,\cdots,\hat{x_i},\cdots,x_n)$. Here $f_1$ and $f_2$ are $C^1$ by the definition of $\partial U$ being $C^1$(see the appendix in Evans).
Remember we want to prove $$\int_U\frac{\partial u}{\partial x_i}dx=\int_{\partial U}u\nu^idS.$$ The description of $U$ above allows us to write the LHS as an iterated integral $$\int_D\left(\int_{f_1(x_1,\cdots,\hat{x_i},\cdots,x_n)}^{f_2(x_1,\cdots,\hat{x_i},\cdots,x_n)}\frac{\partial u}{\partial x_i}dx_i\right)dA,$$ where $dA=dx_1\cdots\hat{dx_i}\cdots dx_n$. Apply the Fundamental Theorem of Calculus to the inner integral, we then have $$\int_Du(x_1,\cdots,f_2(x_1,\cdots,\hat{x_i},\cdots,x_n),\cdots,x_n)-u(x_1,\cdots,f_1(x_1,\cdots,\hat{x_i},\cdots,x_n)\cdots,x_n)dA.$$
This is all we can do to the LHS now. For the RHS, notice that $\partial U$ can be decomposed into three surfaces $S_2$, $S_3$ and $S_{1}$ where $\nu^i$ at all the points of $S_2$ are positive, $\nu^i$ at all the points of $S_3$ are zero ($S_3$ is parallel to the $x_i$ axis) and $\nu^i$ of $S_1$ are negative. Thus, RHS is
$$\int_{S_2}u\nu^idS+\int_{S_3}u\nu^idS+\int_{S_1}u\nu^idS.$$
Since $\nu_i$ for $S_3$ is zero, only the first and last term keep. From the geometric picture described at the beginning, the projection of $S_1$ and $S_2$ onto the $x_1x_2\cdots\hat{x_i}\cdots x_n$ hyperplane are exactly $D$. Also keep in mind that $\nu^i$ is the direction cosine of $\nu$ with the $x_i$ axis in $\mathbf{R}^n$. Therefore, $$\int_{S_2}u\nu^idS=\int_Du(x_1,\cdots,f_2(x_1,\cdots,\hat{x_i},\cdots,x_n),\cdots,x_n)d
A,$$
and $$\int_{S_1}u\nu^idS=-\int_Du(x_1,\cdots,f_1(x_1,\cdots,\hat{x_i},\cdots,x_n),\cdots,x_n)dA.$$
This proves the theorem when $U$ is convex. For general $C^1$ $U$, I am thinking to cut the region into convex chunks so that when we glue them together the surface integral over touching faces are just cancelled due to opposite normal directions. Of course, I hope occasional "non-smoothie" won't introduce too much trouble.