Since Azure Service Fabric is running on "Azure Virtual Machine Scale Sets" you should try to automate the installation. Azure Virtual Machines have a concept called "Virtual Machine Extensions". Software like the "Azure Diagnostics Agent" are automatically installed on each of your nodes through this mechanism.
Since the program you want to install will most likely not be available directly as a Virtual Machine Extension, you could use Azure Automation DSC (Desired State Configuration) to install additional software on your nodes.
DSC needs an agent on your virtual machines, which is available as a Virtual Machine Extension. There is an ARM-based template that shows how you can integrate the extension into a Virtual Machine Scale Set. You can include this extension in your Service Fabric ARM template and re-deploy it to have the extension installed on each of your nodes.
After this, you could use the Package feature of DSC to install your software.
However, be aware that creating this solution might require a considerable amount of time. PowerShell DSC is a very powerful system that, once installed, gives you many more possibilities in terms of server management.