What you're missing is that the two treatments are the same. In the second one, the Brillouin zone is 2 times smaller but
$$ \cos(k+\pi) =-\cos(k)$$
so choosing the opposite sign in front of the energy is equivalent to shifting to the now-forbidden half of the Brillouin zone. When you identify the states correctly, there are of course the same states in both cases.
Note that changing $k$ to $k+\pi$ is equivalent to the alternating sign flips at the lattice sites,
$$ a_m\to (-1)^m a_m $$
in the position representation. Most typically, the original large Brillouin zone may be divided to two – one for which $a_{m+1}$ is closer to $+a_m$ and one-half for which it is closer to $-a_m$ and it's sensible to redefine the sites by the alternating signs. At any rate, the doubling of the states coming from the $\pm$ sign exactly compensates the halving of the Brillouin zone for $k$.