Yeah, that's always been around, in one form or another. It may have originally been part of the Mage's Guild, but it would still have had it's own Archmagister for the Skyrim Branch, and it still would have been known as the College of Winterhold.
The College itself most definately been around since Oblivion, a text makes mention of the College of Winterhold trying to wight back against the Mythic Dawn: http://www.imperial-library.info/content/great-collapse
You know as well as any the College's history and reputation in Winterhold. It has long been a source of pride for your city, a unique fixture in Skyrim. Some of the greatest wizards have studied here, and the College has always promoted positive relations with the other provinces of Tamriel.
It is well-known that those relations have been, shall we say, strained over the last few decades. After the Oblivion Crisis, it was only natural that the people of Skyrim showed a distrust for mages, even though the vast majority of us actively worked to counter the actions of the Mythic Dawn cult. The College expected such a reaction, and hoped that distrust would fade over time.
The first paragraph implies the College has been around for a
long time.
The second implies it has been around since at least
Oblivion.