The most obvious considerations for selling upgrades themselves is to remove the margin they are now paying OptionTown and to not have to award the upgraded cabin points. Although with the new earnings the difference between the various classes is marginal while the point cost of upgrades hasn't been decreased.
Partly perhaps to get more in-line with their partners. On UA you also purchase upgrades directly from them but only get points for the original booking class.
It is a shame that SK keeps killing off successful concepts. First the EB downgrades, now attempts to change this. I can see why passengers feel screwed if their OT gets shot down and then have SK offer the same upgrade at a higher price with fewer perks. If you value OT as a service, I'd recommend you boycott the upgrades SK offers. Either until they stop the initiative or get it right.