The first version of the question asked about just sucking up the atmosphere with a hose, without manipulating gravity. I'll answer that first, since I think it's a very good question that many — including my previous self — get wrong.
No manipulation of gravity
They did this with a giant vacuum cleaner in the movie Spaceballs. But as knzhou comments, it is fundamentally impossible. The reason that the atmosphere stays where it is, is there there is hydrostatic equilibrium: Gravity tries to pull the air molecules down, but pressure builds up and prevents it from collapsing altogether. Whether or not you build a 500 km long hose, doens't change that.
A vacuum cleaner works by creating a lower pressure $P$ inside than outside. But in this case the gravitational potential $\Phi$ is the same inside and outside. In the case of the atmosphere, $P$ is lower in space, but $\Phi$ is lower closer to Earth.
Here a drawing that may help understand. At a given height, $P$ and $\Phi$ is the same inside and outside the hose
Fiercely manipulating gravity
Your first edit assumes that gravity can be manipulated arbitrarily. In that case, there is no limit to how fast the atmosphere can be sucked out. Just create an Alcubierre drive. Essentially this works by constructing a metric of space such that there is gradient that can, in principle, be arbitrarily large. Although the air molecules don't move through space faster than light locally, as seen from "outside" the speed can be faster than $c$.
You'd have to think carefully about how exactly you do this without simultaneously tearing Earth apart.
Moderately manipulating gravity
Your second edit assumes a maximum speed of $v=c/2$. In that case the answer is simply given by the distance from the antipode of the hose (since air on the other side of the Earth from the hose needs to travel around Earth), plus the distance from ground to space. Assuming 500 km for the latter, that distance is roughly $d = 20,\!500\,\mathrm{km}$, so the time is $t=d/c=0.07$ seconds.