First, it's walking whatever the webserver give back as links.
Directories and files are the same thing as far as http goes.
You could exclude those you describe with the -exquery option.
Something like
-exquery="\alpha\=\alpha"
Or you could use -Q to strip all query strings so that
http://sharingfirst.mit.edu/members/team034/videos/?S=D
would be treated as
http://sharingfirst.mit.edu/members/team034/videos/