As much as I love the blood splattered across my furnishings, and the secret room full of rotting flesh and skeletons...

It just isn't very appealing, you know?

Will these vanish eventually?

You can talk to the guy you bought the house from and upgrade components in your home.

How do you get the house? I've been wanting it but I don't want to side with the Stormcloaks.

Secret room full of rotting flesh and skeletons? I would buy a house just for that.

It doesn't matter who you side with.

You should be able to buy any and all houses regardless of your alignment.

If I speak to Jarl Ulfrich the first conversation string I'm forced onto is whether or not to side with them :/

And if I remember correctly, you can simply say: that's not why I'm here and he won't harass you about it.