So they can have their projects hosted at yet another company that Microsoft is going to acquire? Seriously, Microsoft has nothing even close to the capability of Jira. And SourceTree would be a nice addition to Microsoft's collection of developer tools.
Atlassian is a public company with a market cap of $15 billion. I don't think Microsoft is going to acquire them.
You only need a 51% voting share to control a company. $15 billion * 0.51 = what Microsoft just paid for GitHub.