[proofplan]
We compute the Euclidean Laplacian in the spherical coordinate chart by expressing the gradient and divergence in the orthonormal moving frame determined by the coordinate map. The metric scale factors are $1$, $r$, and $r\sin\theta$, so the radial contribution becomes the divergence term $r^{-2}\partial_r(r^2\partial_r\tilde{u})$. The remaining two terms involve only $\theta$ and $\phi$, and they combine exactly into $r^{-2}\Delta_{S^2}\tilde{u}$.
[/proofplan]
[step:Introduce the spherical coordinate map and its scale factors]
Define the spherical coordinate map
\begin{align*}
\Phi: (0,\infty)\times(0,\pi)\times\mathbb{R} &\to \mathbb{R}^3\setminus\{0\}
\end{align*}
by
\begin{align*}
\Phi(r,\theta,\phi)
=
(r\sin\theta\cos\phi, r\sin\theta\sin\phi, r\cos\theta).
\end{align*}
The coordinate derivatives are
\begin{align*}
\partial_r\Phi
=
(\sin\theta\cos\phi,\sin\theta\sin\phi,\cos\theta),
\end{align*}
\begin{align*}
\partial_\theta\Phi
=
(r\cos\theta\cos\phi,r\cos\theta\sin\phi,-r\sin\theta),
\end{align*}
and
\begin{align*}
\partial_\phi\Phi
=
(-r\sin\theta\sin\phi,r\sin\theta\cos\phi,0).
\end{align*}
Their Euclidean lengths are
\begin{align*}
|\partial_r\Phi|=1,\qquad |\partial_\theta\Phi|=r,\qquad |\partial_\phi\Phi|=r\sin\theta,
\end{align*}
and their Euclidean pairwise inner products are zero. Thus the spherical coordinates are orthogonal with scale factors
\begin{align*}
h_r=1,\qquad h_\theta=r,\qquad h_\phi=r\sin\theta.
\end{align*}
[/step]
[step:Write the gradient in the spherical orthonormal frame]
Define the orthonormal frame fields
\begin{align*}
e_r(r,\theta,\phi)&:=\partial_r\Phi(r,\theta,\phi),
\end{align*}
\begin{align*}
e_\theta(r,\theta,\phi)&:=\frac{1}{r}\partial_\theta\Phi(r,\theta,\phi),
\end{align*}
and
\begin{align*}
e_\phi(r,\theta,\phi)&:=\frac{1}{r\sin\theta}\partial_\phi\Phi(r,\theta,\phi).
\end{align*}
Let $v := \tilde{u}=u\circ\Phi$. Since $u\in C^2(\mathbb{R}^3\setminus\{0\})$ and $\Phi$ is smooth on $(0,\infty)\times(0,\pi)\times\mathbb{R}$, the function $v$ is $C^2$ on this coordinate domain.
For a coordinate curve, the chain rule gives
\begin{align*}
\partial_r v=(\nabla u\circ\Phi)\cdot \partial_r\Phi,
\end{align*}
\begin{align*}
\partial_\theta v=(\nabla u\circ\Phi)\cdot \partial_\theta\Phi,
\end{align*}
and
\begin{align*}
\partial_\phi v=(\nabla u\circ\Phi)\cdot \partial_\phi\Phi.
\end{align*}
Using the scale factors and the orthonormal frame, these identities imply
\begin{align*}
\nabla u\circ\Phi
=
(\partial_r v)e_r
+
\frac{1}{r}(\partial_\theta v)e_\theta
+
\frac{1}{r\sin\theta}(\partial_\phi v)e_\phi.
\end{align*}
[guided]
The goal is to express $\nabla u$ in directions adapted to spheres centered at the origin. The coordinate map
\begin{align*}
\Phi: (0,\infty)\times(0,\pi)\times\mathbb{R} &\to \mathbb{R}^3\setminus\{0\}
\end{align*}
sends $(r,\theta,\phi)$ to
\begin{align*}
(r\sin\theta\cos\phi, r\sin\theta\sin\phi, r\cos\theta).
\end{align*}
The function being differentiated in coordinates is
\begin{align*}
v: (0,\infty)\times(0,\pi)\times\mathbb{R} &\to \mathbb{R},
\end{align*}
defined by $v=u\circ\Phi$. Since $u$ is $C^2$ away from the origin and $\Phi$ is smooth on its coordinate domain, $v$ is $C^2$.
The coordinate vector $\partial_r\Phi$ has length $1$, while $\partial_\theta\Phi$ has length $r$ and $\partial_\phi\Phi$ has length $r\sin\theta$. Therefore the corresponding unit vectors are
\begin{align*}
e_r=\partial_r\Phi,\qquad e_\theta=\frac{1}{r}\partial_\theta\Phi,\qquad e_\phi=\frac{1}{r\sin\theta}\partial_\phi\Phi.
\end{align*}
These vectors are pairwise orthonormal. The chain rule says that differentiating $v=u\circ\Phi$ in a coordinate direction computes the directional derivative of $u$ in the corresponding coordinate vector:
\begin{align*}
\partial_r v=(\nabla u\circ\Phi)\cdot \partial_r\Phi,
\end{align*}
\begin{align*}
\partial_\theta v=(\nabla u\circ\Phi)\cdot \partial_\theta\Phi,
\end{align*}
and
\begin{align*}
\partial_\phi v=(\nabla u\circ\Phi)\cdot \partial_\phi\Phi.
\end{align*}
Because $\partial_\theta\Phi=r e_\theta$ and $\partial_\phi\Phi=r\sin\theta\, e_\phi$, the components of $\nabla u\circ\Phi$ in this orthonormal frame are
\begin{align*}
(\nabla u\circ\Phi)\cdot e_r=\partial_r v,
\end{align*}
\begin{align*}
(\nabla u\circ\Phi)\cdot e_\theta=\frac{1}{r}\partial_\theta v,
\end{align*}
and
\begin{align*}
(\nabla u\circ\Phi)\cdot e_\phi=\frac{1}{r\sin\theta}\partial_\phi v.
\end{align*}
Hence
\begin{align*}
\nabla u\circ\Phi
=
(\partial_r v)e_r
+
\frac{1}{r}(\partial_\theta v)e_\theta
+
\frac{1}{r\sin\theta}(\partial_\phi v)e_\phi.
\end{align*}
[/guided]
[/step]
[step:Apply the divergence formula in the same orthogonal coordinates]
Let
\begin{align*}
A: \mathbb{R}^3\setminus\{0\} &\to \mathbb{R}^3
\end{align*}
be a $C^1$ vector field whose spherical-coordinate components in the frame $(e_r,e_\theta,e_\phi)$ are
\begin{align*}
A\circ\Phi=A_r e_r+A_\theta e_\theta+A_\phi e_\phi,
\end{align*}
where
\begin{align*}
A_r,A_\theta,A_\phi:(0,\infty)\times(0,\pi)\times\mathbb{R}\to\mathbb{R}
\end{align*}
are $C^1$. For orthogonal coordinates with scale factors $h_r=1$, $h_\theta=r$, and $h_\phi=r\sin\theta$, the Euclidean divergence is
\begin{align*}
(\operatorname{div}A)\circ\Phi
=
\frac{1}{r^2\sin\theta}
\frac{\partial}{\partial r}(r^2\sin\theta\,A_r)
+
\frac{1}{r^2\sin\theta}
\frac{\partial}{\partial\theta}(r\sin\theta\,A_\theta)
+
\frac{1}{r^2\sin\theta}
\frac{\partial}{\partial\phi}(rA_\phi).
\end{align*}
Apply this to $A=\nabla u$. From the preceding step,
\begin{align*}
A_r=\partial_r v,\qquad A_\theta=\frac{1}{r}\partial_\theta v,\qquad A_\phi=\frac{1}{r\sin\theta}\partial_\phi v.
\end{align*}
Therefore
\begin{align*}
(\Delta u)\circ\Phi
=
\frac{1}{r^2\sin\theta}
\frac{\partial}{\partial r}(r^2\sin\theta\,\partial_r v)
+
\frac{1}{r^2\sin\theta}
\frac{\partial}{\partial\theta}(\sin\theta\,\partial_\theta v)
+
\frac{1}{r^2\sin\theta}
\frac{\partial}{\partial\phi}\left(\frac{1}{\sin\theta}\partial_\phi v\right).
\end{align*}
Since $\sin\theta$ is independent of $r$ and $\phi$, this becomes
\begin{align*}
(\Delta u)\circ\Phi
=
\frac{1}{r^2}\frac{\partial}{\partial r}(r^2\partial_r v)
+
\frac{1}{r^2\sin\theta}
\frac{\partial}{\partial\theta}(\sin\theta\,\partial_\theta v)
+
\frac{1}{r^2\sin^2\theta}\partial_{\phi\phi}v.
\end{align*}
[/step]
[step:Identify the angular part with the spherical Laplacian]
Define the angular differential operator
\begin{align*}
\Delta_{S^2}v
=
\frac{1}{\sin\theta}
\frac{\partial}{\partial\theta}(\sin\theta\,\partial_\theta v)
+
\frac{1}{\sin^2\theta}\partial_{\phi\phi}v.
\end{align*}
Substituting this definition into the formula obtained above gives
\begin{align*}
(\Delta u)\circ\Phi
=
\frac{1}{r^2}\frac{\partial}{\partial r}(r^2\partial_r v)
+
\frac{1}{r^2}\Delta_{S^2}v.
\end{align*}
Since $v=\tilde{u}=u\circ\Phi$, this is exactly the claimed decomposition at every $(r,\theta,\phi)\in(0,\infty)\times(0,\pi)\times\mathbb{R}$. This completes the proof.
[/step]