The mother felt sad about her daughter not being in college.
Literal
Mother [topic-は], university [to-に] entered-not daughter [matter-のこと] [object-を] sadly thought
大学に入っていない娘 = 'daughter who has not entered university' — a negative relative clause modifying 娘. のこと wraps the daughter into a broader concern. さびしく is the adverbial form of さびしい.