I am unable to give a proper answer, but the problem can be somewhat
reduced and the example for $\tau=\sqrt{-7}$ is easy enough to demonstrate.
I give those details in the hope that others can concentrate on the more
intricate matters, such as higher class numbers.
Let us write
$$\begin{align}
\operatorname{E}_4 &= \gamma_2\eta^8
& \gamma_2 &= \mathfrak{f}^8\mathfrak{f}_1^8 +
\mathfrak{f}^8\mathfrak{f}_2^8 -
\mathfrak{f}_1^8\mathfrak{f}_2^8
\\ \operatorname{E}_6 &= \gamma_3\eta^{12}
& \gamma_3 &= \frac{1}{2}\left(\mathfrak{f}^8 + \mathfrak{f}_1^8\right)
\left(\mathfrak{f}^8 + \mathfrak{f}_2^8\right)
\left(\mathfrak{f}_1^8 - \mathfrak{f}_2^8\right)
\end{align}$$
where $\eta$ is the
Dedekind eta function
and $\mathfrak{f},\mathfrak{f}_1,\mathfrak{f}_2,\gamma_2,\gamma_3$ are modular
Weber functions.
Then we can split the task of evaluating the classical Eisenstein series at
complex quadratic irrationals into the following subtasks:
- Evaluate some modular (Weber) function, which gives an algebraic value.
Due to algebraic interrelations, the algebraic nature carries over to
the values of the other modular functions.
- Evaluate the weight-giving eta factor, which introduces a
product of Gamma function values.
Subtask 1 has been routinely done a century ago using modular equations
and transformations, as well as more advanced methods that do not require
knowledge of the modular equation.
Useful exercises and references can be found in [BB87].
As a very easy example, combine e. g. the basic identities for Weber functions
$$\begin{align}
\mathfrak{f}(\tau)\,&\mathfrak{f}_1(\tau)\,\mathfrak{f}_2(\tau)
= \sqrt{2}
& \mathfrak{f}(-\tau^{-1}) &= \mathfrak{f}(\tau)
\\ \mathfrak{f}^8(\tau) &= \mathfrak{f}_1^8(\tau) + \mathfrak{f}_2^8(\tau)
& \mathfrak{f}_1(-\tau^{-1}) &= \mathfrak{f}_2(\tau)
\end{align}$$
with the modular equation
$$ \mathfrak{f}(\tau)\,\mathfrak{f}(7\tau) =
\mathfrak{f}_1(\tau)\,\mathfrak{f}_1(7\tau) +
\mathfrak{f}_2(\tau)\,\mathfrak{f}_2(7\tau)$$
and set $-\tau^{-1} = 7\tau$, then you can deduce
$\mathfrak{f}^3(\tau) = 2\sqrt{2}$.
As an eta quotient, $\mathfrak{f}(\tau)$ takes positive real values
for purely imaginary $\tau$, therefore $\mathfrak{f}(\tau) = \sqrt{2}$.
Then $\mathfrak{f}(\sqrt{-7}) = \mathfrak{f}(-\tau^{-1}) = \mathfrak{f}(\tau)
= \sqrt{2}$.
Ramanujan tabled values of his class invariants $G_n$ and $g_n$
which are closely related to Weber's $\mathfrak{f}$ resp. $\mathfrak{f}_1$
at $\tau=\sqrt{-n}$.
Likewise, in [Web08], which also provides the theory,
the appendix contains a table with Weber's $\mathfrak{f}(\sqrt{-n})$
or $\mathfrak{f}_1(\sqrt{-n})$ for quite many positive integer values of $n$.
From each such value, the corresponding values of the other Weber functions
can be determined algebraically, e. g. for $\tau=\sqrt{-7}$ we arrive at
$$\begin{align}
\mathfrak{f}(\sqrt{-7}) &= \sqrt{2}
& \gamma_2(\sqrt{-7}) &= 255
\\ \mathfrak{f}_{1,2}(\sqrt{-7}) &= \sqrt[8]{8 \pm 3 \sqrt{7}}
& \gamma_3(\sqrt{-7}) &= 1539 \sqrt{7}
\end{align}$$
Subtask 2 may be attempted with a ${}_2F_1$-based representation such as
$$ \eta^2 = \frac{1}{\mathfrak{f}^4}{}_2F_1\left(
\frac{1}{4},\frac{1}{4};1;\frac{64}{\mathfrak{f}^{24}}\right)$$
as presented
elsewhere on this site.
Background for that representation is given in section 5.4 around proposition 21
in [Zag08].
However, reducing that ${}_2F_1$ expression for a given algebraic value of
$\mathfrak{f}^{24}$ to a product of Gamma function values seems a long-winded
and barren, if not outright infeasible, route to me. Roughly speaking,
each value would require some specific sequence of even more specific
${}_2F_1$ transformations, which is the direct opposite to what we actually
want: A general method that does not depend much on the value of $\tau$.
I am entering unfamiliar terrain now, so let's hope I get the facts right.
Subtask 2 seems to have been boosted with a formula by Lerch (1897)
that expresses a certain product of eta function values in terms of
a product of Gamma function values. More than half a century later,
such a thing became known as Chowla-Selberg
formula[CS67].
The eta product therein contains $h(-n)$ eta factors with arguments in
$\mathbb{Q}(\sqrt{-n})$ where $h(-n)$ is the
class number of the ring of integers of $\mathbb{Q}(\sqrt{-n})$.
For $h(-n)=1$, the Chowla-Selberg formula can be used to solve for
the value of a single eta function. In particular, for an odd prime $p$
with $h(-p)=1$, we get
$$\begin{align}
\eta^4(\sqrt{-p}) &= \frac{1}{2\pi p\,\mathfrak{f}^4(\sqrt{-p})}
\left(\prod_{m=1}^{p-1}
\Gamma\left(\frac{m}{p}\right)^{\chi(m)}\right)^{w/2}
\\ &= \frac{1}{(2\pi)^{1+w\frac{p-1}{4}}p^{1-\frac{w}{4}}
\mathfrak{f}^4\left(\sqrt{-p}\right)}
\left(\prod_{\chi(m)=1} \Gamma\left(\frac{m}{p}\right)\right)^w
\end{align}$$
where $\chi(m) = \left(\frac{m}{p}\right)_2$ is the
Legendre symbol, and
$w$ is the number of units in the ring of integers of $\mathbb{Q}(\sqrt{-p})$.
- Note that the above formula for $\eta^4(\sqrt{-p})$ contains
$\mathfrak{f}^4(\sqrt{-p})$, so you still need subtask 1.
Alternatively, note that
$\mathfrak{f}(\tau)\,\eta(\tau) =
(-1)^{-1/24}\eta\left(\frac{\tau+1}{2}\right)$,
therefore the Chowla-Selberg formula gives you
$\eta^4\left(\frac{\sqrt{-7}+1}{2}\right)$ directly.
For $p = 7$ we thus obtain
$$ \eta^4(\sqrt{-7}) = \frac{\Gamma\left(\frac{1}{7}\right)
\Gamma\left(\frac{2}{7}\right) \Gamma\left(\frac{4}{7}\right)}
{56\,\pi\,\Gamma\left(\frac{3}{7}\right) \Gamma\left(\frac{5}{7}\right)
\Gamma\left(\frac{6}{7}\right)}
= \frac{\left(\Gamma\left(\frac{1}{7}\right)
\Gamma\left(\frac{2}{7}\right) \Gamma\left(\frac{4}{7}\right)\right)^2}
{64\,\pi^4 \sqrt{7}}$$
and combining this with the values for $\gamma_2$ and $\gamma_3$ we get
$$\begin{align}
\operatorname{E}_4 &= \frac{255\left(\Gamma\left(\frac{1}{7}\right)
\Gamma\left(\frac{2}{7}\right) \Gamma\left(\frac{4}{7}\right)\right)^4}
{28672\,\pi^8}
\\ \operatorname{E}_6 &= \frac{1539\left(\Gamma\left(\frac{1}{7}\right)
\Gamma\left(\frac{2}{7}\right) \Gamma\left(\frac{4}{7}\right)\right)^6}
{1835008\,\pi^{12}}
\end{align}$$
as you have mentioned.
For $h(-n)>1$, the remaining problem was to isolate individual
eta values from the product. Steady progress has been made to overcome
the intrinsic limitations of earlier methods.
Let me refer you to [Har04] or [CH05] for a method that builds on results
by Williams et al., van der Poorten, Chapman, and Hart from around 2000.
I have not looked into it, so I cannot tell whether this
method also improves subtask 1, or uses it as a building block, or both.
References
[BB87] J. M. Borwein and P. B. Borwein: Pi and the AGM, Wiley 1987,
ISBN 0-471-83138-7.
[CH05] R. Chapman and W.B. Hart: Evaluation of the Dedekind eta function.
In: Canadian Mathematical Bulletin 49 (2006), pp. 21-35.
DOI: 10.4153/CMB-2006-003-1.
[CS67] S. Chowla and A. Selberg: On Epstein's zeta function.
In: Crelles Journal für die reine und angewandte Mathematik 227 (1967),
pp. 86-110. Available online.
[Har04] W. B. Hart: Evaluation of the Dedekind Eta Function.
PhD thesis 2004, Macquarie University, Sydney.
[Web08] H. Weber: Lehrbuch der Algebra, Vol. III. In german.
AMS Chelsea Publishing, 3rd edition 1961, ISBN 0-8218-2971-8.
Reprinted 2001, 1st edition 1908.
[Zag08] Don Zagier: Elliptic modular forms and their applications.
In: Kristian Ranestad (ed.): The 1-2-3 of modular forms. Springer 2008,
DOI: 10.1007/978-3-540-74119-0.