Credits to Francesco Polizzi for putting me on the right track, by pointing to Deligne's work.
The important references for this are
I guess if one invokes perverse sheaves there might be more general answers. If anyone would like to give such a more general answer, I would be very grateful!
[Edit] As Dan points out below, working with perverse sheaves indeed helps: then there is a decomposition if $f$ is proper. [/Edit]
What follows requires that $f$ is smooth (and proper, which was already an assumption in the question). Here goes my attempt:
The decomposition
In Deligne's thesis “Théorème de Lefschetz et critères de dégénérescence de suites spectrales” we find the following results:
- Proposition 2.1 states that in the derived category $D^{\textrm{b}}(\bar{Y})$ we have an isomorphism
$$ \textrm{R}f_{*} \mathbb{Q}_{\ell} \cong \bigoplus_{i} \textrm{R}^{i}f_{*} \mathbb{Q}_{\ell}[-i]. $$
The proposition applies, since $\mathbb{Q}_{\ell}$ satisfies the Lefschetz condition by the relative hard Lefschetz theorem (this uses that $f$ is smooth and proper).
- Proposition 2.16 with $Z = \textrm{Spec}(k)$, can be applied (since $Y$ is smooth over $k$; and by the previous point). This gives
$$ \textrm{R}(\Gamma f)_{*} \mathbb{Q}_{\ell} \cong \bigoplus_{k} \textrm{R}\Gamma_{*} (\textrm{R}f_{*}^{k} \mathbb{Q}_{\ell}[-k]). $$
Taking the $n$-th homology group, then gives
$$ \textrm{H}^{n}(\bar{X}, \mathbb{Q}_{\ell}) = \bigoplus_{q} \textrm{H}^{n}(\bar{Y}, \textrm{R}f_{*}^{q} \mathbb{Q}_{\ell}[-q]) = \bigoplus_{q} \textrm{H}^{n-q}(\bar{Y}, \textrm{R}f_{*}^{q} \mathbb{Q}_{\ell}). $$
This last expression can of course be written in the usual way:
$$ \textrm{H}^{n}(\bar{X}, \mathbb{Q}_{\ell}) = \bigoplus_{p+q=n} \textrm{H}^{p}(\bar{Y}, \textrm{R}f_{*}^{q} \mathbb{Q}_{\ell}). $$
The Galois equivariance
If I am not mistaken, the above decomposition is Galois equivariant. I hope some expert can point out errors if I go astray. Here it goes:
- Deligne starts with a very general Proposition (1.2) where he works with the bounded derived category $D^{\textrm{b}}(A)$ of some abelian category $A$. In particular we can work with the category $D^{\textrm{b}}(Y \times_{k} \bar{k})$ of lisse $\mathbb{Q}_{\ell}$-sheaves together with the Galois action. Here one has to identify $\sigma^{*}\mathcal{F}$ with $\mathcal{F}$, just as when one defines the Galois action on $\ell$-adic cohomology (or when proving the functoriality of $\textrm{H}_{\textrm{ét}}^{i}(\_, \mathbb{Q}_{\ell})$).
- The next Theorem we need is (1.5), and this is Galois equivariant because the hard Lefschetz theorem is Galois equivariant. (Here I bluf that this also holds for the relative hard Lefschetz theorem.)
- Consequently the decomposition of Proposition 2.1 is Galois equivariant.
- And finally, therefore the decomposition of Proposition 2.16 is also Galois equivariant.