Let the object be the system under consideration and $\hat r$ the unit radial vector point outwards from the centre of the Earth.
The attractive gravitational force on the object due to the Earth $\vec F = \frac{GMm}{R^2} (-\hat r) = -\frac{GMm}{R^2} (\hat r) $ is the external force acting on the system.
$-\frac{GMm}{R^2}$ is the component of the gravitational force in the $\hat r$ direction.
The displacement of this force is $\delta \vec r = \delta r (\hat r)$ where $\delta r$ is the component of the displacement in the $\hat r$ direction.
The work done by the gravitational force undergoing a small displacement $\delta \vec r$ is $\vec F \cdot \delta \vec r = - \frac{GMm}{R^2}\, \delta r$.
The sign of this quantity depends on the sign of the component of the displacement in the $\hat r$ direction.
So the total work done by the gravitational force is $\displaystyle \int^{\rm R}_{\rm R+h} -\frac{GMm}{R^2}\,dr$ which works out to be a positive quantity.
So positive work is done on the object and this is equal to its change in kinetic energy.
Stepping back from this integral you have a negative quantity $-\frac{GMm}{R^2}$ multiplied by a series of negative quantities $\delta r$ which will generate a positive value for the work done on the object by the gravitational force due to the Earth.
The other thing to note is that you are correct in writing the left hand side integral as $\int_0^V v\,dv$ because you ahve taken $V$ to be the component of the velocity in the $\hat r$ direction.
If you analysed the motion and found a value for $V$ you would find it to be a negative quantity ie the velocity is in the $-\hat r$ direction.
This is difficult to show in this situation but let me illustrate what happens if the gravitational field strength $\vec g = - g\hat r$ is constant.
The equation of motion of the mass is $m \frac {d\vec v}{dt} = m\vec g \Rightarrow \frac {dv}{dt} \hat r = - g\, \hat r \Rightarrow \frac {dv}{dt} = -g $
From this you get $\displaystyle \int _0^V dv = \int _0^t -g \,dt \Rightarrow V = -g\,t$ and you "know" the final velocity will be downwards.
If $t$ is positive then $V$, the component of velocity on the $\hat r$ direction is negative ie downwards.