Something is very badly wrong with your calculations. Even putting aside that if you want to raise the orbit of something, you need to thrust in the direction of travel.

But to actually calculate the energy requirements you need to first treat the problem in terms of momentum
- You want to change the velocity of Phobos by 1mm/s
- That requires sending some mass in the opposite direction
- The required change in momentum is $0.001m/s\times10^{16}kg$ = $1\times10^{13}kg\cdot m/s$
- Lets say the electric drive has an exhaust velocity of 20km/s
- The amount of propellant required is thus $\frac{10^{13}kg\cdot m/s}{2\times10^4m/s}=5\times10^8kg$
So a change in velocity of 1mm/s, would require firing 500000t of propellant at 20km/s in the other direction. This happens to be about equal to the mass of a supertanker or the Empire State Building.
Now that we know we need to fire out 500000t/s at 20km/s we can calculate the energy requirements using $E=\frac{1}{2}mv^2$ (hint: it's going to be bad). It is simply equal to $$0.5\times5\times10^8\times20000^2 = 10^{16}J$$
This amount of energy is roughly equal to the energy unleashed in the detonation of a fairly large thermonuclear warhead. So we actually could impart a change in velocity of 1mm/s on Phobos, altough we would need to nuke it, which would not save it from falling apart.
Phobos is huge. It's tiny on the scale of moons and planets, but it's still huge relative to things humans build and manipulate. If you take all the coal which is mined every year - which is about 5 billion tonnes, Phobos is 2000 times bigger than that. So even dismantling it into pieces to be flung out of a high powered electric mass driver would be a monumentally huge task.