It's the Show Package Contents option on the View menu that leads to packages (including application bundles) being displayed and treated as folders:
If you want to keep this behavior, and are still running Finder, you can do the following:
Open Path Finder » Set Menu Keys… and navigate to the Commands » Open With… » Running » Finder menu item. Press
Cmd-Ctrl-1 or any other shortcut you want to use for this. Press it to run a selected application even with Show Package Contents checked by "opening" it via Finder.
You could also create a simple "Launcher" application e.g. in Automator that receives an path to an
.app as argument and
opens it. Then you don't need to keep Finder running. Setting up a keyboard shortcut in Path Finder works just like with Finder, except you don't choose the entry from the running applications list.