Thank you so much for the feedback. It is very important for us and we take into account these kind of cases to improve our stacks.
As we compile Apache, PHP and other components for the stack and we only include in the stack the result of the compilation you won't be able to compile new versions of any component. This is oriented for production environments. That is the reason why we recommend the users to migrate to a new stack of Wordpress instead of trying to install php/apache by their own.
It is not required to update the entire stack each time we release a minor version of Wordpress including minor versions of components like Apache/Mysql/PHP. You can update Wordpress to the next minor versions using the Web wizard.
In case of major updates of Wordpress or security issues in any of the components we post a new entry in http://blog.bitnami.com/ telling the users to upgrade.
In your case each time you want to make a migration to a new stack you can backup the configuration files of Wordrpress/Apache and restore them in the new stack just to simplify a bit more the manual task.
As I said before, thank you so much for the feedback. We will consider creating a new stack with Wordpress preconfigured with SSL by default.