I think you have the right idea.
When you define $F(t,u)$, you really mean
$$ \frac{\partial}{\partial u} F(t,u) = f(t,u) $$
I confess I prefer the notation $F_2(t,u)$, where "$F_2$" means "the derivative of $F$ with respect to its second argument" for reasons that will be made clear shortly.
So you computed the integral correctly and got that the limit is
$$ \lim_{t \to 0} \frac{F(t, ct) - F(t, -ct)}{t} $$
and it's the right idea that this looks very much like a limit for computing a derivative.
If we were asked to compute the limit
$$ \lim_{u \to 0} \frac{F(t, cu) - F(t, -cu)}{u} $$
then this is indeed equal to
$$ \lim_{u \to 0} \frac{F(t, cu) - F(t, -cu)}{u} = 2c F_2(t, 0) = 2c \frac{\partial}{\partial u} F(t,u) \mid_{u=0} $$
(Notice how awkward partial derivative notation is becoming!) But that's not actually what we're computing! Your idea of computation is effectively to compute
$$ \lim_{t \to 0} \lim_{u \to 0} \frac{F(t, cu) - F(t, -cu)}{u} $$
but the thing we actually want to compute can be written as
$$ \lim_{t \to 0} \lim_{u \to t} \frac{F(t, cu) - F(t, -cu)}{u} $$
Are we sure these are equal? The answer would be yes if the following limit exists:
$$ \lim_{(t,u) \to (0,0)} \frac{F(t, cu) - F(t, -cu)}{u} $$
Alas I'm rusty on my analysis. There's probably some theorem that says this should definitely be true because $F(t,u)$ is continuously differentiable in a neighborhood of $(0,0)$, but it doesn't spring to mind.
So I'll get my hands dirty and do a differential approximation. Rather than prove the full theorem, I'll do just the limit we're interested in
$$ \lim_{t \to 0} \frac{F(t, ct) - F(t, -ct)}{t} $$
$$ = \lim_{t \to 0} \frac{F(0,0) + t F_1(0,0) + ct F_2(0,0) - F(0,0) - t F_1(0,0) + ct F_2(0,0) + o(t) }{t} $$
$$ = \lim_{t \to 0} 2c F_2(0,0) + o(1) = 2c F_2(0,0) = 2c f(0,0)$$
where I've used little-oh notation to represent the error terms conveniently. It's clear from this calculation why we need $f$ to be differentiable! And you should check that $F(t,u)$ is also continuously differentiable.