Thanks - that does sound like a big advantage of the deb / rpm route. Plus you don't really want your app servers spending their CPU time compiling.
For example, for our deployment, we rely on softlinks and uwsgi robust reload behavior to avoid losing requests. I've seen many devops who were using hg update/git update as a way to "deploy" (arg!), but I'm not sure about the behavior of deb/rpm.
And you’re right: replacing files of a running application can lead to all kind of weirdness. I’d even prefer to lose some requests than to risk that.