This is not a proof, just some tips that can may be leads to a proof
(I really hope someone manage to find a proof for this result)
You can consider the other form for the exponential integral:
$$Ei(z)=\gamma +\ln(x)+\sum_{k=1}^\infty\frac {x^k}{k\cdot k!},$$
where $\gamma$ is the Euler-Mascheroni's constant.
Call the $n$-th non trivial zero
$$p_n=:\frac 12 +i \alpha_n.$$
So you get
$$Ei(p_n)=\gamma +\ln\left(\frac 12 +i \alpha_n\right)+\sum_{k=1}^\infty\frac {\left(\frac 12 +i \alpha_n\right)^k}{k\cdot k!}.$$
Use the principal determination of the complex logarithm: $\ln(x+iy)=\ln(x)+i\arg(x+iy)$, where
$$\arg(x+iy)=\arctan\left(\frac yx\right).$$
So
$$Ei(p_n)=\gamma +\ln\left(\frac 12\right) +i\arctan(2\alpha_n)+\sum_{k=1}^\infty\frac {\left(\frac 12 +i \alpha_n\right)^k}{k\cdot k!}.$$
So
$$\mathfrak I(Ei)(p_n)=\arctan(2\alpha_n)+\sum_{k=1}^\infty\left(\sum_{\substack{m=0 \\ m\equiv 1 (4)}}^{k}\frac {\binom km\alpha_n^m}{2^{k-m}k\cdot k!}-\sum_{\substack{m=0 \\ m\equiv 3 (4)}}^{k}\frac {\binom km\alpha_n^m}{2^{k-m}k\cdot k!}\right),$$
using
$$\binom km=\frac{k!}{m!(k-m)!}$$
you get
$$\mathfrak I(Ei)(p_n)=\arctan(2\alpha_n)+\sum_{k=1}^\infty\left(\sum_{\substack{m=0 \\ m\equiv 1 (4)}}^{k}\frac {\alpha_n^m}{2^{k-m}k\cdot m!(k-m)!}-\sum_{\substack{m=0 \\ m\equiv 3 (4)}}^{k}\frac {\alpha_n^m}{2^{k-m}k\cdot m!(k-m)!}\right).$$
The key is to use now the approximation:
$$\alpha_n\approx \frac{2\pi n}{\ln(n)}$$
to put $\pi$ in the place.
To conclude, you have to prove that
$$\lim_{x\to \infty}\frac 1x\sum_{n=1}^x\mathfrak I(Ei)(p_n)=\pi.$$
For the first term, you can say that
$$\frac 1x\sum_{n=1}^x \arctan(2\alpha_n)=\frac 1x\left(\text{a finite number of terms}\right)+\frac 1x(x-K)\left(\text{something close to $\frac\pi2$}\right),$$
so
$$\lim_{x\to \infty}\frac 1x\sum_{n=1}^x \arctan(2\alpha_n)=\frac\pi 2.$$
Now, you need to deal with the second term, you can use Stirling formula
$$y!\sim \sqrt{2\pi y}\frac{y^y}{e^y}$$
to get
$$\frac {\alpha_n^m}{2^{k-m}k\cdot m!(k-m)!}=\frac{(2\pi n)^m e^m e^{k-m}}{\ln(n)^m 2^{k-m}k\sqrt{2\pi m}m^m \sqrt{2\pi(k-m)}(k-m)^{k-m}}$$
$$=k\left(\frac{2\pi n}{m\ln(n)}\right)^m\left(\frac e{2(k-m)}\right)^{k-m}\sqrt{2\pi k}.$$