The company I work at is very careful about keeping our intellectual property on our infrastructure, and I am surprised that a larger company like Microsoft doesn't have similar policies.
It would be highly contradictory for MS to take the position, as a matter of policy, that it is too risky for them to ever place confidential business data onto a third party cloud-hosted SaaS system, because that is precisely the risk they are asking every one of their customers to take.
Similarly, if you have concerns about putting your company's source code into GitHub now, you should be equally concerned about putting your company's prerelease annual report on the office365 onedrive.
That is a good point though, it’s becoming more and more inconvenient for a company to self host everything. Microsoft does stand to benefit from everyone becoming more accustomed to relying on 3rd party services in the cloud.
Essentially, choose your vulnerability: cloud provider single point of failure or in-house lack of resources
It depends on how important the code is.
I don't imagine MS will ever move Office or Windows to external servers, but a lot of other stuff is fair game.
There is always a security/convenience trade off.