You can put MobileTerminal.app on your iPhone, and any new app that you install using iPHUC, or whatever, you'll need to open Terminal.app and chmod +x the executable, for instance ... if you install Zune2.app, you'll need to open Terminal.app and:
chmod +x /Applications/Zune2.app
The only problem, though, is that you need to chmod Terminal.app before you can use it! So you either need SSH, SFTP or both. There is a way of installing Installer.app which is a package manager that automatically downloads programs and installs them for you if you choose them, and it can update your apps ... I highly recommend putting it on there. Anyway, there's an automated installer for it that doesn't require chmod +x and doesn't require SSH.
Here's the thread about it:
https://forums.macrumors.com/threads/344240/
But yeah, you can put the program ON your phone without SSH, you just can't run the program until the permissions are set correctly.