While St. Valentine's Day does coincide with the festival of Lupercalia, the idea of Valentine's Day as a romantic festival is a much later one. It's worth pointing out that according to Plutarch, the 'striking' of women done during the Lupercalia festival was done largely symbolically on the hands of willing 'victims' with strips of skin from sacrificed animals, rather than a bunch of blood-crazed Romans running around punching the first woman they see. The extent to which this is a 'dark origin' is therefore down to personal interpretation. The Lupercalia itself was popular within the city of Rome until the 4th Century, and seemingly reached parts of Northern Italy and Southern Gaul, but does not appear to have necessarily been a widespread phenomenon throughout the Empire as a whole.

The article you linked actually does provide the likely origin of the modern, romantic (if not Romantic) Valentine's Day, but skips past it without looking: Chaucer. Chaucer's late 14th Century poem Parliament of Fowls (written essentially 1000 years after the suppression of the Lupercalia in Rome) is the first work to credit St. Valentine's Day with romantic connotations. Parliament of Fowls is a humorous poem that takes a philosophical look at love, and was most likely composed to celebrate the engagement of Richard II with Anne of Bohemia. In particular, the Valentine's Day connotations come from this line:

For this was on seynt Volantynys day

Whan euery bryd comyth there to chese his make".

Andy Kelly argues that this "Valentine's Day" is actually far more likely to be the feast of St Valentine of Genoa, the 3rd of May, an argument lent substantial weight by the simple fact that February is considerably early for migratory bird populations to have returned and begun nesting, while nests would be full or even fledging in May. Over time, it's likely that Chaucer was simply misinterpreted, or that his poem was actively conflated with the other Saint Valentine, given his vita includes his performing of marriages. The connection with Lupercalia therefore is more likely to be mere coincidence.