Rigorously speaking, yes, you are right if dealing with the Lagrangian function. Indeed E.-L. equations should be more properly written
$$\frac{d}{dt} \left(\frac{\partial L}{\partial \dot{q}^k}\right) - \frac{\partial L}{\partial {q}^k}= 0\:, \quad \frac{d q^k}{dt} = \dot{q}^k\quad k=1,\ldots, n\:.$$
In other words $\dot{q}^k$ becomes $\frac{d q^k}{dt}$ just along the solutions of the equations but, otherwise $\dot{q}^k$ and ${q}^k$ are independent variables.
This is because, geometrically speaking, $L$ is a map from the first jet bundle $j^1(S)$ where $T: S\to \mathbb R$ is the fiber bundle called spacetime of configurations, the basis $\mathbb R$ represents the axis of time whereas every fiber $T^{-1}(t)$ is the configuration space at time $t$. Natural local coordinates adapted to the fiber bundle structure are the standard coordinates $t, q^1,\ldots, q^n$.
The jet bundle $J^1(S)$ adds kinematic coordinates $\dot{q}^1,\ldots, \dot{q}^n$.
In this picture the identity, in local natural coordinates,
$$\frac{df(q(t),t)}{dt}=\sum_{k=1}^n\frac{\partial f}{\partial q}(q(t),t)\dot{q}^k(t) + \frac{\partial f}{\partial t}(q(t),t)$$
makes sense along the solutions of EL equations, but it does not without fixing a curve $q=q(t)$ (solution of EL equations or not) because the derivative in the left-hand side cannot be computed.
Nevertheless the formalism is constructed just to encourage this intuitive and effective interpretation since, after all it is quite harmless. One may define
something like $$\widetilde{\frac{df(q,t)}{dt}}=\sum_{k=1}^n\frac{\partial f}{\partial q}(q,t)\dot{q}^k + \frac{\partial f}{\partial t}(q,t)\:,$$
without fixing a section of $S$. As soon as a solution of EL is given, the notation becomes consistent with the standard one.
It is important to stress that if focusing on the action rather than the Lagrangian, in order to implement the variational principle, it is correct to always identify $\dot{q}^k$ with $\frac{dq^k}{dt}$, since the action is a functional over a space of curves and $\dot{q}^k=\frac{dq^k}{dt}$ is always assumed to be valid on each of theses curves no matter if they satisfy EL equations or not.