In my humble opinion, great IDs are problem solvers at their core. Working with branding guidelines is part of a common problem, and usually isn't difficult to solve.
The scenario in which all eLearning being produced within an organization looks and feels like a disjointed conglomeration of random learning products, each with its own completely distinct flavor, is harmful to the big picture of a learning organization as well.
I don't disagree that branding guidelines certainly are not designed with eLearning (or any learning) in mind, but I do think that it becomes an easy/lazy excuse for not coming up with a solution. I've yet to see a company that uses the guidelines to say that every color must unreasonably be within their palette (re: "I don't care if trees are green, our colors are blue and orange!"), or that has font restrictions that impede learning.
Option 2 provides the most reasonable approach. More work, but the best IDs will always relish that challenge.