This community-wiki answer is compiled from the comments.
One way to define a category of compactifications for an individual space $X$ is to consider the objects to be all compactifications of $X$, and a morphism from one compactification $\alpha : X \to K$ to another one $\beta : X \to L$ to be a continuous map $f : K \to L$ such that $f\alpha=\beta$. This does define a category.
With an extra condition on $X$ (completely regular), the Stone-Čech compactification is indeed an initial object. It is constructed by letting $F$ be the set of continuous maps $f : X \to [0,1]$, embedding $X \hookrightarrow [0,1]^F$ so that the $f$-the component is equal to $f$, and taking the closure of the image of $X$. One proves that it satisfies the universal property defining an initial object.
Also this answer shows that under a further restriction on the definition of compactification, one can prove that the one-point compactification satisfies the universal property required to be a terminal object. As stated in that link, the extra restriction on a compactification $\alpha : X \to K$ is that $\alpha(X)$ must be open in $K$ and that every compact subset of $K$ must be closed. This condition can be attained by a further restriction on $X$, namely that $X$ be a locally compact, noncompact Hausdorff space.