Hi,
Based on my experience, when using RDP into the windows operating systems VMs in Windows Azure, it is not possible to boot into the safe mode as it seems that
RDP cannot work in safe mode.
In addition, since you cannot RDP into that VM, I recommend you to check the endpoint for remote PowerShell and follow the link below to connect to that VM via remote PowerShell, then using windows
powershell cmdlets to uninstall Xenapp.
Remote PowerShell in Azure IAAS Virtual Machines
In addition, where did you install Xenapp? If it is in D:\ and there is no important data in D:\, maybe you can resize the VM to see if the issue persists.
Best regards,
Susie