I feel conflicted about my parents paying off one of my students loans
what sort of conflict is it about?
It just don't feel right to me, but they want to help him out
They're your parents so they want to help you for your own good. Be gracious about it and you can find a way to really thank them later.
What if it's not my choice and I feel like crap about it?
It is still good to show appreciation for the help that you are receiving, especially when it is such generous assistance.  If you have the means to do so, insist that you still make your own payments, even with your parents also helping.  Tell them that this is only to save on interest and pay it off sooner, and find a way to pay them back later on.