This answer is wrong. You should use @whpowell96's comment instead.
More precisely, the part where I restrict the integral to $[0,\frac 1 n]$ is false because $e^{0} = 1$ so the integral on $[\frac 1n, 1]$ is worth $1-\frac 1n$. The infimum of $F$ over $X \cap C^2$ is not $0$. It seems to be a positive value which is maybe hard to compute, and it might be hard to construct explicit sequences $u_n$ such that $F(u_n) \to \inf_{X \cap C^2} F$.
First, for every $u \in X \cap C^2$, you have $F(u) \geq 0$ (because both terms in the integrand are positive). And in fact, $F(u) > 0$. Indeed, $F(u) = 0$ would imply that the integrand is zero everywhere so $u(x) = 0$ on $[0,1]$, but you have the boundary condition $u(0) = 1$.
Second, let us show that there exists a sequence $u_n \in X \cap C^2$ such that $F(u_n) \to 0$. For this let us take any function say $v \in C^\infty(\mathbb{R}_+;\mathbb{R})$ with $v(0) = 1$, $v' \leq 0$ on $\mathbb{R}_+$ and $v$ compactly supported in $[0,1)$ (so $v$ and all its derivatives vanish at $1$). In particular $0 \leq v(x) \leq 1$. And we set $u_n(x) := v(nx)$ for $n \in \mathbb{N}^*$. Then you have $u_n(0) = 1$, $u_n(1) = 0$ and $u_n \in C^\infty$. Then
$$
\begin{split}
F(u_n) & = \int_0^1 e^{-|u_n'(x)|} + u_n^2(x) \mathrm{d}x \\
& = \frac{1}{n} \int_0^{\frac{1}{n}} e^{-n |v'(nx)|} + v^2(nx) \mathrm{d} (nx) \\
& = \frac{1}{n} \int_0^1 e^{-n |v'(y)|} + v^2(y) \mathrm{d} y \\
& \leq \frac{2}{n}.
\end{split}
$$
To conclude, $F$ does not have a minimizer $u^*$, because the only possible value would be $F(u^*) = 0$, which is not achieved.