It seems like the consensus here is that the easiest way to approach the problem would be to use Weyl's Equidistribution Theorem (the technique used to get the answer given on the MIT website). Though here is another approach I wrote up yesterday, based on the fact that the partial sum in question can be decomposed into a Fourier series expansion and some additional terms:
$$\sum_{k=1}^N|\cos(k)|=\frac{2N}{\pi}+\frac{|\cos(N)|-1}{2}-\frac{2}{\pi}\sum_{m=1}^\infty\frac{(-1)^m}{4m^2-1}\frac{\sin(2mN)}{\tan(m)}$$
The proof I wrote went as follows:

Though unfortunately I made an error when I assumed $\sum_{m=1}^\infty\frac{1}{m^2|\sin(m)|}$ converges, because whether or not the sum actually does converge is still an open problem. Which if you happen to be interested in, you could look at: Are there any series whose convergence is unknown? for a more thorough discussion. Though even proving that the full error term converges in the original series seems to require more advanced knowledge about facts concerning the Diophantine approximation of $\pi$. Though if it can be proven then as seen above this would give the much stronger result:
$$\sum_{k=1}^N(|\cos(k)|-\frac{2}{\pi}) \text{ } \text{ Is bounded as } N \text{ tends to infinity}$$
So I would guess that probably the only simple way of attacking this problem would be using Weyl's Theorem or at least something similar because it doesn't seem all that straight forward to solve using other techniques.
EDIT : The problem actually can be solved this way. If you divide both sides by $N$ and apply the dominated convergence theorem, the error term $\text{S}$ will tend to zero, giving your required result. Though this just wont give you the stronger expression I posted above.