This quest illustrates the adage "No good deed goes unpunished"
I don't think the quest is as black and white as people assume.
If your objective is to side with someone who'll cause less casualties. Siding with Roy leads to the deaths of more people. Many more actually.
If your objective is to get back at the elitist "bastards" in Tenpenny Tower, Roy is exactly like them in attitude. He even wants to blow up Megaton because its a "Smoothskin rat-hole."
There's really no reason to side with Roy if you want to go for the "good" ending.