It isn't that hard to manage your applications as individual installs; we've been doing so for years.
That said, I recommend planning to migrate over to docker or LXC for a couple reasons:
- Security
While docker by default isn't ideal on security, there's some benefit to isolating an application to a container, as if it's compromised it can limit the exposure from being able to impact other parts of your server.
- Dependency management
Your package manager might do just fine with the services you have, but the more you try to run, the more complex a problem dependency management can become, and some important upgrade can cause unforseen consequences on another service.
- Rapid prototyping
On the future if you want to try something new, it's easy to spin up a docker container for some bleeding edge service, and if it doesn't work, you can drop the docker image and be confident that the application has made no changes to your filesystem, and you aren't going to run into some weird problem down the line because you installed and uninstalled something you've since forgotten.