Actually docker was created to enable easy scaling of web applications. If you want to package your application up take a look at some modern package managers. By using a modern package manager like nix you can work around the issues of containers while still keeping the "it just works" advantage of containers.
This does not mean that containers are bad, it's just that using a good package manager is usually a simpler solution.
Take a look at my blog post if you want to read more on this: http://www.mpscholten.de/docker/2016/01/27/you-are-most-like...