Here is a step by step how to do this:
1. Backup SCCM and Windows Server.
2. Uninstall Software update point and WSUS
3. Disable SMS_Executive, SMS_Component_Manager services (this is not required, but I did this).
4. Restart Windows.
5. Upgrade Windows Server 2012 R2.
6. Enable, set startup type to Automatic and start these services "World Wide Web Publishing Service" and "Windows Process Activation Service"
7. Got to IIS Manager -> Application Pools. You will see following picture:
For "Classic .NET AppPool" select v2.0 in ".NET CLR Version" field for others select the v4.0.
8. Install WSUS and this hotfix https://support.microsoft.com/en-us/kb/3095113 to add Windows 10 upgrades installation possible.
9. Start SCCM services, install Software update point.
10. Install Windows Updates.
11. Check in SCCM Component Monitoring that everything works.