Let us try to obtain a counterexample. We assume that $u$ is sufficiently smooth.
Let us write the variational definition of the first eigenvalue:
$$
\mu_1[u] = \inf_{\eta \in W_0^{1,2}(\Omega)}\frac{\int_\Omega |\nabla \eta|^2 \,dx - \int_\Omega \nabla \cdot (u \eta) \, \eta \,dx}{\int_\Omega |\eta|^2 \,dx}, \quad \left( \eta \not\equiv 0 \right).
\tag 1
$$
For the second integral in the numerator we have
$$
\int_\Omega \nabla \cdot (u \eta) \, \eta \,dx =
\int_\Omega (\nabla \eta \cdot u) \, \eta \,dx +
\int_\Omega \eta^2 (\nabla \cdot u) \,dx.
\tag 2
$$
Auxiliary, we note that integration-by-parts formula gives us
$$
\int_\Omega \eta_{x_i} u_i \, \eta \,dx =
-\int_\Omega \eta \, u_i \, \eta_{x_i} \,dx - \int_\Omega \eta^2 (u_i)'_{x_i} \,dx,
$$
(here we used the fact that $\eta = 0$ on $\partial \Omega$).
Therefore,
$$
\int_\Omega \eta_{x_i} u_i \, \eta \,dx = -\frac{1}{2}\int_\Omega \eta^2 (u_i)'_{x_i} \,dx.
$$
Using this equality, for the first integral on the rhs of $(2)$ we derive
$$
\int_\Omega (\nabla \eta \cdot u) \, \eta \,dx = \sum_{i=1}^n \int_\Omega \eta_{x_i} u_{i} \, \eta \,dx = -\frac{1}{2} \int_\Omega \eta^2 \sum_{i=1}^n(u_i)'_{x_i} \,dx =
-\frac{1}{2} \int_\Omega \eta^2 (\nabla \cdot u) \,dx.
$$
Hence, for $(2)$ we have
$$
\int_\Omega \nabla \cdot (u \eta) \, \eta \,dx = \frac{1}{2} \int_\Omega \eta^2 (\nabla \cdot u) \,dx \geq \frac{1}{2} \min_{\Omega} (\nabla \cdot u) \int_\Omega \eta^2 \,dx = C \int_\Omega \eta^2 \,dx.
\tag 3
$$
Finally, for $(1)$ we obtain
$$
\mu_1[u] \leq \inf_{\eta \in W_0^{1,2}(\Omega)} \left( \frac{\int_\Omega |\nabla \eta|^2 \,dx - C \int_\Omega \eta^2 \,dx}{\int_\Omega |\eta|^2 \,dx} \right) =
\inf_{\eta \in W_0^{1,2}(\Omega)} \left( \frac{\int_\Omega |\nabla \eta|^2 \,dx}{\int_\Omega |\eta|^2 \,dx} - C\right) = \lambda_1 - C \leq 0
$$
for any $C \geq \lambda_1$ (it is possible, due the fact that we have no a priori assumptions on $\nabla \cdot u$). Here $\lambda_1$ is the standard first eigenvalue of the Dirichlet Laplacian in $\Omega$.
(Note also that the first inequality is true, since it is true for any $\eta \in W_0^{1,2}(\Omega)$).
Using the inverse inequality for $(3)$ we obtain the condition for the strict positivity of $\mu_1[u]$: $\max_{\Omega} (\nabla \cdot u) < 2 \lambda_1$. (consequently, if $\nabla \cdot u \leq 0$, as you wrote.)
P.S. Actually, I can not figure out right now is the variational characterization correct. But in any case, if we assume that the first eigenfunction is "normal", then the construction above holds (without taking $\inf$).
\triangleby\Delta. – Did Jun 14 '16 at 12:46