Let us denote by $C$ the standard complex conjugation of functions on a Hilbert space $H:=L^2(X)$.
It is already false that the eigenvalues of $C$ are $\pm 1$.
First of all, from $C\psi = \lambda \psi$ you have $CC\psi = \overline{\lambda} C\psi = |\lambda|^2 \psi$. Since $CC=I$ and $\psi\neq 0$, we conclude that $|\lambda|=1$ and not $\lambda = \pm 1$.
Furthermore, suppose that $\psi \neq 0$ is a real ($L^2$) function and consider $\phi_\alpha:= e^{i\alpha} \psi$ for a given real $\alpha$. In this case
$$C\phi_\alpha = e^{-i\alpha} C\psi = e^{-i\alpha} \psi = e^{-2i\alpha} e^{i\alpha}\psi \:.$$
In summary, $$C\phi_\alpha = e^{-2i\alpha} \phi_\alpha\:.$$
So that there are also eigenvectors with arbitrary unit complex eigenvalue and not only $\pm 1$.
Notice also that the complex combination of eigenvectors with a given eigenvalue are not eigenvectors (unless the coefficients of the combination are real) so that the notion of eigenspace is more delicate (it makes sense only referring to real combinations).
It is also false that eigenvectors with different eigenvalues are orthogonal as a trivial consequence of the construction above: $\phi_\alpha$ and $\phi_{\alpha'}$ are not orthogonal if $\alpha\neq \alpha'$, but the eigenvalues are different if $\alpha-\alpha' \not \in 2\pi \mathbb{Z}$.
This failure prevents us from obtaining a complete orthogonal decomposition of vectors in terms of all the eigenvectors of $C$. However, it is possible to have complete expansions in terms of some eigenvectors if the Hilbert space is separable.
As a matter of fact there is a Hilbert basis of eigenvectors with eigenvalue $1$.
Let $N:=\{u_n\}_{n\in \mathbb{N}}$ be a Hilbert basis (countable because the Hilbert spece is assumed to be separable).
Then we can always extract another Hilbert basis made of real functions, thus eigenvectors of $C$ with eigenvalue $1$.
To this end, decompose every $u_n$ into real and imaginary part and form a new set of vectors
$M:=\{\mathfrak{R}\left(u_n\right), \mathfrak{I}\left(u_n\right)\}_{n\in \mathbb N}$ (some of these vectors may be $0$!).
The $L^2$ scalar products of pairs of vectors in $M$ are real by construction.
Therefore the standard orthogonalisation procedure of Gram-Schmidt yields a new orthonormal set of real vectors $N'$.
Since the finite complex linear combinations of $N$ are the same as those of $N'$, we conclude that the complex span of $N'$ is dense in $H$. In other words $N'$ is a Hilbert basis of $H$, made of eigenvectors of $C$ with eigenvalue $1$. (But it does not mean that $H$ is the eigenspace of $C$ with eigenvalue $1$ as it would happen for bounded linear operators, avoinding the contradiction $C=I$!)
All the discussion can be extended to generic Hilbert spaces $H$ for antilinear operators $C:H\to H$ satisfying $CC=I$.