It's fine. W32Time (Windows Time) is now a "trigger start" service, where before in earlier versions of Windows it used to run 24x7.
You should have no problem relying on the virtual machine time integration service.
Or, if Azure doesn't utilize the VM IC time integration service, you could take this document as evidence of how your Azure VM would be expected to synchronize its time if it hasn't been configured to do otherwise:
License Terms for Windows Azure.doc:
• Windows Time Service. This service synchronizes with
time.windows.com once a week to provide your computer with the correct
time. You can turn this feature off or choose your preferred time
source within the Date and Time Control Panel applet. The connection
uses standard NTP protocol.
But if you still want to set up your own custom NTP config anyway, you are totally free to do so if you wish. Just set the Windows Time service to Automatic, then issue a command such as:
w32tm /config /manualpeerlist:"0.us.pool.ntp.org 1.us.pool.ntp.org" /syncfromflags:manual /update