What's there to be confused about? Their stance on Bitcoin is getting clearer and clearer the way I see it. They've already said that they don't plan on banning it, choosing to go the regulation route, and now they've ruled that it has value, and can therefore be confiscated.
Seems to me like they do accept its integration with society, for as long as it's not abused by shady individuals. South Korea is a major cryptocurrency market, and it's looking like it will continue to be. The crackdowns are just noise; most of these have already been done by countries like the US (regulation of exchanges, taxation, seizing Bitcoins, etc.).
To summarize the regulatory measures introduced by the South Korean government as one sentence, it can be summed up as "the principle of prohibition, the actual operation of the main regulatory."