Yes. If $a$ and $b$ are generators of $\mathbb F_2$ then $\mathcal R \rtimes_\alpha \mathbb F_2$ decomposes as an amalgamated free product of $(\mathcal R \rtimes_\alpha \langle a \rangle)$ and $(\mathcal R \rtimes_\alpha \langle b \rangle)$ over $\mathcal R$, where each of these are hyperfinite. Brown, Dykema, and Jung showed in http://arxiv.org/abs/math/0609080 that for separable finite von Neumann algebras being embeddable into $\mathcal R^\omega$ is stable under amalgamated free products over a hyperfinite von Neumann algebra. Thus $\mathcal R \rtimes_\alpha \mathbb F_2$ is embeddable into $\mathcal R^\omega$, which is equivalent to QWEP. Induction then gives the case when $2 \leq n < \infty$, and the case $n = \infty$ then follows since QWEP is preserved under (the weak-closure of) increasing unions.

Related to this, Collins and Dykema in http://arxiv.org/abs/1003.1675 have recently shown that the class of Sophic groups is stable under taking amalgamated free products over amenable groups.

I believe this is an open problem however if we consider arbitrary residually finite groups instead of only $\mathbb F_n$.