I can't say I quite understand what you're saying as I'm coming from the point of veiw that Tes or at least Skyrim is very linear, no choices, nothing changes, it's always the same.
I don't see how adding an option to join Harkon makes the game MORE linear, it would actually add something to it. I have around 7 different characters as I stop around 100 hours and I can honestly say I've done the main quest about 1.5 times! It was great the first time but why would I want to re-do it if I'm going through the exact same events the exact same way?
Also, i'm using linear in the terms of "it's always the same" Or "this is someone else's story laid out for me to play".
The story is linear, but the game is still a sandbox game. With all the radiant AI running and whatnot? Imagine The next TES game without an open world, and without AI that does what it wants to do on it's own...all scripted/predictable. THAT is what I meant by linear.
People assume since the story is linear, the game is linear. But you don't take into account that you don't have to the MQ/DG at all...and still put up 300+ hours, or more, and just play/role play. Sand box game personified. Break that down into linear fashion...AKA corridor fashion...Or may like Dragon Age 2. The illusion of have a sand box game, but it really isn't...Just so we can have choices to blow up a town. Corrupt a city forever. Or something real drastic. That would instantly kill the TES series (corridor/DA 1/2 type approach).
The way the game is designed, Mass effect type game alterations wouldn't work in Skyrim, or a large scale sand box game. There's a reason why we only see these choices on a large scale, on games that are very linear. ME 1, 2, 3, DA 1,2. It's easier to make the alterations for 1. And the AI isn't as hard to code for. Can you imagine coding radiant AI in towns, if you want to alter towns (blow them up or what ever)? It would be a mess... Took them forver to get it going, Radiant AI.