I'm sure you could, but bear in mind that several OS X Server services are built on top of the system Apache and its configuration file structure, so you probably don't want to replace it with a package manager-built version if you rely on any of these services.
On the other hand, it wouldn't be too hard to build and install a version of the SSL module compatible with the system Apache linked against a newer OpenSSL version, however, and I wouldn't expect this to break Apple's services, at least not until you install an update that either breaks binary module compatability or clobbers your tweaked module configuration.
I don't use Homebrew, so I couldn't tell you if it's capable of building modules for the system Apache, but building the SSL module "by hand" for system Apache with Homebrew OpenSSL should be straightforward enough.
On the other hand, it wouldn't be too hard to build and install a version of the SSL module compatible with the system Apache linked against a newer OpenSSL version, however, and I wouldn't expect this to break Apple's services, at least not until you install an update that either breaks binary module compatability or clobbers your tweaked module configuration.
I don't use Homebrew, so I couldn't tell you if it's capable of building modules for the system Apache, but building the SSL module "by hand" for system Apache with Homebrew OpenSSL should be straightforward enough.