Not really.
If you play the other game with mouse/KB then you can unplug the controller after starting PSO, so PSO only registers controller inputs for most things.
If you play PSO with mouse/KB then you can unplug the controller prior to running PSO then it won't pick it up.
If you want to play both games with a controller, then you'll have to do convoluted remapping for both games so one of them sees the controller as keyboard/mouse inputs but not a controller. This also probably makes your keyboard useless when playing otherwise.
Or the other game you're playing supports more than one controller, which is cool but means you need another controller, and runs the risk of Windows getting confused which controller is player 1.