Stencyl is good for creating flash games as well. And it doesn't require for you to code, but you do have to create your own art and such. Also, it'll take some time to create a quality game with Stencyl if you're planning on submitting a game on Armor Games.
The file type. If your file is called "game" then it should look like "game.swf".
And now to answer your questions before you ask them. If you made it in game maker it is not a SWF. If you made it in game maker you can not submit it. If you made it in game maker there is no possible way to convert the file to a SWF.
Stencyl isn't harmful towards your computer at all. According to WOT (Web-Of-Trust) and AVG (antivirus), it isn't harmful. And about Stencyl "stinking". If you want to create a quality game with it, then it'll take time. If you want to create a quick game, it'll take a day to a week. Well, if you don't want to use Stencyl, have fun learning how to code properly.
