Then I was talking to a security engineer at my company, who pointed out that a VM would make him feel better about the whole thing anyway. And it occurred to me: if I packaged it as a VM, then I'd get both isolation and determinism. It would be easier to install and easier to debug.
So that's why I decided to go with a Vagrant-based installation. The obvious downside is that it's harder now to integrate it with external systems or to use the full power of whatever environment you deploy it in.