Is there any way I can use the launcher without keeping it in my freespace 2 folder? It gets kind of annoying having to go through computer to gog to freespace 2 every time I want to launch the game.

You can make a desktop alias/shortcut of it.

Right click the application file, there should be a command saying "create shortcut" near the bottom of the list above "Delete" and "Rename". Click "create shortcut" and a shortcut should be created. Drag the shortcut to the desktop. There should be two other options there as well: pin to task bar and pin to start menu. Those will essentially create shortcuts in your task bar and start menu respectively.

It would be easier to select Send To... from the right-click menu and choose Desktop (Create Shortcut) from there.