Where did you go wrong?
According to you the work done must be positive because you are evaluating $|\vec F| \cos 0 |d\vec s|$ and all three terms in that expression are positive.
The magnitude of $\vec F$, $|\vec F|$, must be equal to the positive quantity $\dfrac{GMm}{r^2}$ as $r>0$ so $\vec F = \dfrac{GMm}{r^2} (- \hat r)$
$d\vec s = |d\vec s| (-\hat r) = ds (-\hat r)$
This gives $\vec F \cdot d\vec s = \dfrac{GMm}{r^2} (-\hat r) \cdot ds (-\hat r) = \dfrac{GMm}{r^2}\, ds$ with $ds$ positive as it is the magnitude of $d\vec s$.
So to use this expression you must have $ds$ positive ie any integration must be one where $r$ increases unless you substitute $(-dr)$ for $ds$.
If you deal with components rather than magnitudes you do not run into the same problem.
Let us start with $\vec F \cdot d\vec s$ which in your case is the work done by the gravitational force when the mass $m$ is displaced by $d \vec s$.
Let $\hat r$ be the unit vector in the positive r-direction.
$\vec F = F \,\hat r$ and $d \vec s = dr\, \hat r$ where $F$ and $dr$ are components of $\vec F$ and $d \vec s$ in the $\hat r$ direction.
$\vec F \cdot d\vec s = F \,dr $
In your example $\vec F = -\dfrac{GMm}{r^2}$ and $dr$ is yet to be determined.
So what is the sign of $\vec F \cdot d\vec s = F \,dr = -\dfrac{GMm}{r^2} \, dr$?
That all depends on the sign of $dr$ which can either be positive or negative.
What determines the sign of $dr$?
The limits of integration will determine the sign of $dr$ during the process of integration.
In your example you move the particle from $r_1 \hat r$ to $r_2 \hat r$.
It does not matter at this stage whether $r_1 > r_2$ or $r_1 < r_2$ what you need to do is the integration.
$\displaystyle \int _{r_1}^{r_2} -\dfrac{GMm}{r^2} \, dr = GMm\
\left (\dfrac {1}{r_2} -\dfrac {1}{r_1} \right )$ and this is a positive quantity if $r_1 > r_2$.