It may have been a virtue, or indeed, de rigueur (=required by etiquette or current fashion) to be 'prim and proper' in Victorian times, but it is far from a positive comment on someone since the flapper age (1920's good-time girls). For a girl not to down pints of beer, or be shocked by swearing, may seem 'positive' qualities in the girl; but when such a girl is considered 'prim and proper', the image is one of a starchy, formal, unsmiling Sunday School teacher, who thinks fun and play for children should be limited in case they get 'over-excited', and who could never 'let her hair down'. Think of Lady Bracknell in The Importance of Being Ernest as your common garden variety back in those times.
Obviously, you will rarely find this stereotype in its full blown manifestation in the modern world; but it is certainly a negative evaluation of a person, and still connotes a very staid person who can't take a joke and doesn't really know how to have fun. She must maintain what she considers to be a 'lady-like' demeanor at all times.
Of course, one has to balance that against who is calling the girl prim and proper. The kind of girl a group of football hooligans might term Miss Prim and Proper, (a girl who won't go into a Wet T-Shirt competition down at the pub), we might see as a really nice girl.
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