How to Integrate the Differential Equation for the Pendulum Problem
There is a tidy trick for that using chain-rule. Remember this once and for all. We have
$$\ddot \theta (t) + {g \over l}\sin \left( {\theta \left( t \right)} \right) = 0$$
where it is a nonlinear second order differential equation. Wow, it seems scary a little as we don't have linearty. This is how we tackle this down
$$\ddot \theta (t) = {{{d^2}\theta } \over {d{t^2}}} = {d \over {dt}}\left( {{{d\theta } \over {dt}}} \right) = {d \over {d\theta }}\left( {{{d\theta } \over {dt}}} \right){{d\theta } \over {dt}} = \dot \theta {d \over {d\theta }}\left( {\dot \theta } \right) = {d \over {d\theta }}\left( {{1 \over 2}{{\dot \theta }^2}} \right)$$
then put this into the equation and integrate with respect to $\theta $.
I just want to say one more thing. When you use the work-energy theorem, you directly obtain the integrated form you wanted. Do you know why this happens? It's because the work-energy theorem is nothing more than integrating the second newton law. If you dig into the proof of work-energy theorem for a particle, you may understand what I mean.
Multiply the equation through by $\dot{\theta}$:
$$\dot{\theta}\, \ddot{\theta} +\frac{g}{\ell} \dot{\theta} \sin{\theta} = 0$$
Integrate with respect to $t$.
$$\int dt \, \dot{\theta}\, \ddot{\theta} = \int d\dot{\theta} \, \dot{\theta} = \frac12 \dot{\theta}^2 + C$$
$$\int dt\, \dot{\theta} \sin{\theta} = \int d\theta \, \sin{\theta} $$
It follows from the chain rule,
$$ \frac{d}{dt} = \frac{d\theta}{dt} \frac{d}{d\theta} = \dot{\theta} \frac{d}{d\theta},$$
$$ \ddot{\theta} = \dot{\theta}\frac{d}{d\theta} \dot{\theta} = \frac12 \frac{d}{d\theta} \left( \dot{\theta}^2 \right). $$
I didn't like the above too much as an undergraduate because it looks like ana abuse of notation. One way to think about it is if the path is monotonic, then I can parameterize the derivative in terms of the value of $\theta$, i.e., it is possible to write $\dot{\theta}=g(\theta)$.
Another way of thinking about it is a change of variable in integration. We can change $t\rightarrow \theta(t)$ so long as $\theta$ is monotonic.
$$ \int \ddot{\theta} dt \rightarrow \int \ddot{\theta} \dot{\theta} d\theta = \int \frac12 \frac{d}{dt}(\dot{\theta})^2 d\theta$$