there are several ways to verify whether or not it's an alias or whether you dragged the actual folder to the desktop
does the icon of the folder on the desktop have the word "alias" as part of it's name? is there a little arrow on the icon? if you press "apple key + i" it will tell you if it's an alias (shown at "kind" under "general")
if it's an alias, then you can trash it.....but make sure you didn't drag the original of the folder to the desktop before you trash it