So, let's take some closed loop enclosing a surface $S$ within the fluid and see how the magnetic flux through that loop changes as the loop gets carried along by the fluid. Over a time interval $dt$, $S$ moves a distance $\vec{v} \cdot dt$ and ends up as $S'$. The change in the flux is
$$d\Phi=\int_{S'} \vec{B}(t+dt) \cdot d\vec{a} \; - \int_{S} \vec{B}(t) \cdot d\vec{a} \;$$
Now, since $\vec{\nabla} \cdot \vec{B} = 0$ always, we can integrate $\vec B(t+dt)$ over the closed surface formed by the three surfaces $-S$, $S'$ and $R$ (the surface between $S$ and $S'$) taken together, then use the divergence theorem (this might be the "kind of Stoke's theorem" you were thinking of) to obtain
$$\int_{V} \vec{\nabla} \cdot \vec{B}d^3\vec{r} \; = \int_{S'} \vec{B}(t+dt) \cdot d\vec{a} \; + \int_{R} \vec{B}(t+dt) \cdot d\vec{a} \; - \int_{S} \vec{B}(t+dt) \cdot d\vec{a} = 0\;$$
($V$ is the volume enclosed by the three surfaces). Then, our preceding equation becomes
$$d\Phi=\int_{S} \vec{B}(t+dt) \cdot d\vec{a} \; - \int_{S} \vec{B}(t) \cdot d\vec{a} \; - \int_{R} \vec{B}(t+dt) \cdot d\vec{a} \; = dt\int_{S} \frac{\partial \vec{B}}{\partial t} \cdot d\vec{a} \; - \int_{R} \vec{B}(t+dt) \cdot d\vec{a} \; $$
The differential area $d\vec{a}$ is a parallelogram bounded by a line element $d\vec{l}$ around the loop $\partial S$ and the distance vector $\vec{v} \cdot dt$, so
$$d\vec{a}=d\vec{l} \times \vec{v} \cdot dt$$
Meaning that integrating over $d\vec{a}$ is equivalent to adding up these area elements as we move around the loop. That is, our second term becomes
$$ \int_{R} \vec{B}(t+dt) \cdot d\vec{a} \; = \oint_{\partial S} \vec{B} (t+dt) \cdot (d\vec{l} \times \vec{v} \cdot dt) = dt \oint_{\partial S} \vec{B} (t) \cdot (d\vec{l} \times \vec{v})$$
Where I have taken a first order approximation in the last step. Finally, after some arrangement, we recover the expression you were asking for:
$$\frac{d}{dt}\Phi=\int_{S} \frac{\partial \vec{B}}{\partial t} \cdot d\vec{a}\; + \oint_{\partial S} \vec{B} (t) \cdot (\vec{v} \times d\vec{l})$$
Interestingly enough, and since you asked, Alfvén's theorem can be interpreted in terms of material curves, and the ideal induction equation can be written as a material derivative. See this notes for more details (section 2.1: Physical interpretation of MHD). Also, notice the resemblance between Alfvén's and Kevin's circulation theorem in inviscid fluid dynamics.
