We're planning to work on a new project that'll use Azure Web Apps, we are also trying to adhere to Helix. Since by default Azure Web Apps needs VS to do the deployment, is there a solution to deploy Helix based projects?
Helix is just an software architecture pattern, it has nothing to do with how should be deployed. Your statement
Since by default Azure Web Apps needs VS to do the deployment
is not true. My adivce would be to create separate web deployment packages and deploy them using msdeploy, from your Release management solution, not directly from Visual Studio.
At the end of this blogpost you can find out how to deploy a webdeploy package: