The mother felt lonely with her daughter away at university.
Literal
Mother [topic-は], daughter [subject-が] away [sequential-て] university [to-へ] is-going [because-ので] lonely feeling [object-を] did
離れて大学へ行っている = 'has gone away to university (and is still there).' ので gives the reason. さびしい思いをする = 'to have a lonely feeling' — a set expression for experiencing loneliness.