Since Winter '15 it has been possible to deploy Apex classes even when they are actively scheduled jobs:
An option has been added to the Deployment Settings page that lets you deploy components referenced by active Apex jobs. With this option, you don’t have to cancel Apex jobs to be able to have a successful deployment.
I recently noticed that this only seems to work when using the Metadata API -- when I switch my IDE (MavensMate running on Atom) to use the Tooling API, I start to get these errors again.
Is this the expected behavior or a bug with the Tooling API in my org? If this is the expected behavior, has anyone seen signals from SF on whether they will update the Tooling API to match this behavior? Seems like the kind of thing that should be consistent across tools...