The ends absolutely can justify the means, YES!
let me ask you; if they had used one of the things you mentioned, zoo animals, etc.. would you have gotten up in arms? or was it just because it was political?
(if it was 2 years ago and they looked at GWB would you have cared.

)
if the teach doesn't go back and use the scopes again, shame on them, but I can see the point of teaching the way they did...
For what it's worth, I went through Gaudet many moons ago... and am fully into science as a career...