Okay so I've been avoiding the main quest since I like a dragon free world, and I have been working on Discerning the Transmundane. I realized that I need septimus alive to do the main quest. My question is: Can I just pick up the elder scroll early (Since I'm in Blackreach) before being told about it, or do I have to go through each step to get it so it prevents breaking the main quest?

I have not had any problems when I grab it ahead of time.
The only thing I do watch for is Mzark showing up in the map when I exit. When Mzark does not show up, I have trouble gathering samples for the second part of Discerning the Transmundane, the harvest option will not show up when I activate the NPCs'.

Thanx

Brad's already covered it, but I'd also like to add in that if you just get the Elder Scroll during "Discerning the Transmundane," you can just show it to Paarthurnax when he brings it up so you won't even have to go back to Winterhold or anything. Just make sure you finish all you'd like to do in Blacksreach before starting that quest, or it tends to get kind of broken as hell in there.