I'm afraid the equation
$\cos (\pi A) = E - 2A, \tag{1}$
where $A$ is an orthogonal matrix, cannot hold, at least in the stated generality. To see a counterexample, consider the matrix
$J = \begin{bmatrix} 0 & -1 \\ 1 & 0 \end{bmatrix}, \tag{2}$
and look at $\cos (\pi J)$. Since
$J^2 = -E, \tag{3}$
it is easy to show that, exactly as in the case of $e^{i \theta} = \cos \theta + i \sin \theta$ where $\theta \in \Bbb R$, the real numbers (and in fact for $\theta$ complex as well), we have
$e^{\theta J} = (\cos \theta) E + (\sin \theta) J; \tag{4}$
in fact the demonstration of (4) may be had by means of the power series expansion of $e^{\theta J}$, which, by virtue of (3), looks frighteningly similar to that of $e^{i \theta}$; a more thorough discussion of this proof may be found in my answer to this question. In any event, having (4) in hand, and observing that $J$ is in fact orthogonal, since $J^T = -J$ so that $J^TJ = -JJ = -J^2 = E$, we see that
$e^{\pi J} = (\cos \pi) E= -E = \begin{bmatrix} -1 & 0\\ 0 & -1 \end{bmatrix}, \tag{5}$
but
$E - 2J = \begin{bmatrix} 1 & 2 \\ -2 & 1 \end{bmatrix}, \tag{6}$
yielding another specific counterexample, in addition to that of user7530 in his/her answer to this question. And of course the above is quite similar in spirit to the comment of Olivier Begasset, which provided some, but not all, of the inspiration for my efforts here.
Hope this helps. Cheerio,
and as always,
Fiat Lux!!!