Preliminary commentary :
If your initial constraints are written under the form :
$$\begin{cases}a \sin a=2(1-\cos a)\\ \sin a=\frac12a(1+\cos a)\end{cases}$$
Using classical trigonometric formulas, this system boils down to
$$\begin{cases}\frac{a}{2}\cos \frac{a}{2} = \sin \frac{a}{2} \iff \tan b = b\\ \sin \frac{a}{2}=\frac{a}{2} \cos \frac{a}{2} \iff \tan b = b\end{cases}$$
with $b=\frac{a}{2}=\frac12\beta_n \ell$.
So, your two first equations contain the same information, i.e. that the
$$r_n:=\frac12\beta_n l$$
are the roots of equation $$\tan x = x$$ which has an infinite number of solutions (with $x_n\approx (2n+1)\pi/2$ for large $n$ : draw a graphical representation...).
which amounts to say that :
$$\begin{cases} \cos(\frac12\beta_n \ell)-\frac{2}{\beta_n \ell}\sin(\frac12\beta_n \ell)&=&0\\
\cos(\frac12\beta_m \ell)-\frac{2}{\beta_m \ell}\sin(\frac12\beta_m \ell)&=&0
\end{cases}$$
Let us now prove that :
$$I_{mn}:=\int_0^{\color{red}{\ell/2}} \underbrace{(\cos \beta_nx-\frac2{\beta_nl}\sin \beta_nx)}_{e_n(x)}\underbrace{(\cos \beta_mx-\frac2{\beta_ml}\sin \beta_mx)}_{e_m(x)}dx=0$$
[take care to the $\color{red}{\ell/2}$ !]
Please note that
$$e''_m(x)=-(\beta_m)^2e_m(x) \ \text{and} \ e''_n(x)=-(\beta_n)^2e_n(x)$$
A classical technique in such questions is double integration by parts formula :
$$\int_a^{b} u v'' dx = \int_a^{b} u'' v dx + \begin{cases}+ u(b) v'(b) \\- u(a) v'(a)\\ - u'(b) v(b) \\ + u'(a) v(a)\end{cases}$$
Let us take in the previous formula
$u(x)=e_n(x), \ \ v(x)=e_m(x), \ \ with \ \ a=0,b=\ell/2,$
we obtain the following expression (in which *** are for unimportant factors)
$$\int_0^{\ell/2} e_n e''_m dx = \int_0^{\ell/2} e''_n e_m dx +\begin{cases} + \underbrace{(\cos(\frac12\beta_n \ell)-\frac{2}{\beta_n \ell}\sin(\frac12\beta_n \ell))}_{= 0} \ \times \ (***) \\
- (-2/\ell) \\
+ (***) \ \times \ \underbrace{(\cos(\frac12\beta_m \ell)-\frac{2}{\beta_m \ell}\sin(\frac12\beta_m \ell))}_{= 0}\\
-2/\ell
\end{cases}$$
The previous identity can be written :
$$\underbrace{\int_0^{\ell/2} e_n (-\beta_m^2)e_m dx} = \int_0^{\ell/2} (-\beta_n^2)e_n e_m dx + 0$$
As $\beta_n \ne \beta_m$, this proves that
$$\int_0^{\ell/2} e_n e_m dx = 0$$
Important remark : This issue can be turned, in the setting of Sturm-Liouville theory, into an eigenvalues/eigenfunctions problem where the $r_n$s (as defined above) are eigenvalues of a certain self-adjoint operator associated with a system of orthogonal eigenfunctions, the $e_n$s, which is a natural way to interprete your integral equal to zero.
("self-adjoint" qualificative refers naturaly to the property $\int u''v=\int uv''$ we have obtained above).