"The university is invading their habitat, not the other way around."
Actually, Thompson Woods (where the deer attacks took place) is right in the middle of the campus. It's a tiny little area with paths going through it to get from one side of the campus to the other. Students use the paths, for the most part, to get to class.
The article says the deer are losing habitat to construction projects. The deer are just doing what deer and all animal species do: protecting their young.