Question: I'm looking at deploying some software via GPSI and the current version of the software is distributed as a .exe so I need to convert it to an MSI file.

furthermore, why does MS still distribute some of its software (WMI Tools) as .exe

Answer: 
Check out WinINSTALL LE:

<https://www.softpile.com/wininstall-le/>

You have to install the program, and it will watch what happens and create an MSI installer. I usually make my installs on a clean VM so that it doesn't catch background activities of programs I usually use.
I copy here two lists from a couple of webpages I found.

A long list of deployment software, including repackagers, with descriptions added: <http://www.installsite.org/pages/en/tt_corp.htm>

Here I copy only the names mentioned in this webpage:

* AdminStudio
* Advanced Installer Architect
* AppDeploy Repackager
* Asdis
* CapaInstaller ezMSI
* BMC Software
* MSI Package Builder
* NetInstall
* Network Software Scanner
* Packaging Robot
* Prism
* Radia
* RayPack
* Real Packaging
* RemoteExec
* Remote Installer
* Smart Packager

One more list from: <http://www.interfacett.com/blogs/exe-msi-deploy-exe-based-installer-microsoft-world/>

Probably not all of them are repackagers.

* WinInstall
* wItem Installer (also called Installer2Go)
* VMWare ThinApp
* EXE to MSI Converter (exetomsi.com)
* AppDeploy repackager
* Exemsi MSI Wrapper (exemsi.com)
* Advanced Installer (advancedinstaller.com)