Personally I think the College of Winterhold cause the Great Collapse, they thought the city of Winterhold was overshadowing them and so they thought "Why not destroy all of it and make ourselves the main attraction of the hold of Winterhold.
The College of Winterhold has no interest in being "the main attraction of Winterhold". It's not Disneyland. It's a private institution of academia and higher learning that values it's privacy which is one of the reasons Farelda stops the player character at the walkway to the College to question what his or her business is with the College and why Savos Aren states:
Savos Aren said:
The College is a place where we can focus on that [proper respect and study of magic], without the pressures of the world weighing down on us.
In addition, because of the stigma associated with magic in Skyrim, the only ones that would be interested in traveling to the College are those that want training as mages and those that wish to study documents in the Arcaneum such as the Ysmir Collective. The collapse of an entire city would do nothing to change that. If anything it would have a negative effect because the conveniences of a thriving capital city are no longer available to those that might travel to the College. The position that the College deliberately murdered the population of an entire city for a non-existent ambition isn't particularly credible.
I initially thought he meant an accident in terms of what got the Augur lodged beneath the College, but it makes more sense (to me anyway) that this is a statement about the Great Collapse.
While an accidental experiment in general is a more plausible theory for the College being the cause of the Great Collapse, the general consensus is that the accident to which Tolfdir refers to regarding the Augur was his loss of corporeal form and taking the form of an orb of light. In the context the statement is made that makes the most sense.
In general it makes no sense at all for anyone from the College to disclose that the College caused the Great Collapse by accident, a least not so early in the College of Winterhold quest line. The official position of the College is that the Great Collapse was a natural disaster and that the College of Winterhold was spared due to protective magic that had been in place long before the Great Collapse.
On the Great Collapse by Arch-Mage Deneth said:
That the College has remained unaffected is only a testament to the protective magicks placed around it so long ago. It in no way implies that we were somehow prepared specifically for this event, and is certainly no indication that the College was somehow responsible.
Savos Aren said:
The Great Collapse, as it has come to be known. An unfortunate natural disaster that ravaged the area. The College fared far better than the city of Winterhold, but it was not left untouched...No one is sure of the cause. Some believed the eruption of Red Mountain had far-reaching consequences that were only felt years later. I know there are some who have blamed the College, said that we were responsible. I assure you this is not the case...The Sea of Ghosts practically came alive. No one was expecting it. Monstrous waves battered the shore for weeks on end. Winterhold was ancient and weathered, but it couldn't withstand the sea's fury. Entire districts of the city were lost overnight. The waves receded in time, but the damage was irreversible. Most residents of Winterhold abandoned what was left of the city. The College survived, and so here we remain
If the College did in fact cause the Great Collapse, the player's character at that point is still unproven and therefore not ideally trustworthy of such a guarded secret. It's not exactly the kind of revelation that one of the instructors is going to make casually and in such a vague manner as if it's common knowledge. A more appropriate time would be after the player becomes Arch-Mage but no such revelation ever materializes. My thoughts are that it was a natural disaster because it sounds like one by description. Alternatively if it was caused by something that happened at the College, it was something which no one was aware of or perhaps only Savos Aren, to be passed on to his successor which never happens due to his untimely death.
