To avoid mixing up the concentrations in the numerator, remember that as a reaction runs, concentration drops over time. Therefore, the initial value $[\text{A}]_0$ is always larger than the later value $[\text{A}]_t$. To keep $k$ positive, it must be $(\text{Larger} - \text{Smaller})$, or $[\text{A}]_0 - [\text{A}]_t$!