No, I understand it isn't the obvious choice. I usually went there after my do everything character had been there, since I knew where it was. I do wish there were other ways of getting in to learn the location, and I find it rather offensive that my scholar is not allowed in just because she doesn't want to join some silly college.
Yup I was in the same boat, hated the idea that all the guards started treating my warrior like a spellcaster just cause he asked some info from a mage.
Thing is though that I'd still have no idea that part was skippable unless someone told me. Quests usually have to be done in steps, and I assumed that Septimus' door would be locked or something like that, and the game would require me to do the quest in the proper order.
On a related note, I'm now lugging around an undroppable ivory claw and Gaulder fragment necklace and can't complete the quest since I need access to Saarthal, which can't happen unless I join the college. If the game would at least be a bit consistent about how it lets us approach quests, I could walk in there without needing to be babysat by the old guy in the college, but since the door is locked that's not gonna happen.