KeSPA has traditionally been an incredibly insular organization. They want to make sure everything passes by them for approval of some kind before it gets taken seriously. They are composed of representatives from the teams and sponsors, approve all the leagues and tournaments they like, and dole out the progamer certifications that allows you to play in any KeSPA sanctioned event. Up until SC2, that strategy has worked completely. Anything that wasn't given that label of a "KeSPA approved title" died off on its own relatively quickly because of a lack of support from various avenues. SC2 is arguably the first title to survive and eventually thrive in Korea even without KeSPA support, showing the strength of the title and the resilience of GOMTV.
It is important to note that the power KeSPA has is largely symbolic in Korea, they tend to enforce their will simply through supporting or not supporting it publicly. If they don't support something, teams and players tied to KeSPA are pressured to not associate with that thing. This is what happened with GOM's original league, the GSL in Brood War. It is at least partially true with SC2 as well, many KeSPA-card-carrying pro players who decided to move on to SC2 were not looked upon well and had their progamer status revoked even as they were "retiring" from the organization.
If they had embraced SC2 from the get-go they very likely would have denied any of these new SC2 players rights as progamers, and even if they sanctioned the GSL, they would have done so only if they had heavy influence in the way it was run. It's likely they would have simply moved over their current system of allowing new progamers into SC2 (amateurs could get their pro-card by winning extremely challenging courage tournaments and pro-teams could pick up those they liked the most or even get players that weren't yet pros and develop them).
But this all seems to be changing now that they have decided to partner up with the a much bigger and established SC2 scene as equals. Still, there is a lot of technicalities and traditions that they are going to have to work around to incorporate a fully fledged scene. It seems like they know the scene is way too developed to simply take over the way they normally might want to, so they seem to be trying to compromise.