A lot of couples can't sleep without each other, it's okay for you to slip off to the bathroom but if your gone more then 20, the other person automatically wakes up. My boyfriend is this way, I slip out of bed, and I know he's still asleep, I go out to the living room, which is down stairs, and about 20 minutes later, I hear feet shuffling and look up to see him peek in. I think this is extreamly cute, though annoying at times.
I simply just switched my workout times, as my BF works all sorts of crazy hours, I hate, when he gets two hours a sleep then I wake him up by leaving the bed before he has to go back to work. As I just can't see that being fair or very nice to the other person your living with.
Now if it's the noise that is bothing your SO, make sure you don't have the TV up very loud. Don't do step, don't drop your weights, a lot of times we are very noisy exercisers. Most people get into working out, and they really have no idea how loud they are, until they've been tape recorded. And that might be an idea just to see how loud you are, if you have an old tape recorder, place it in your bedroom and then go workout and then come back and see how much it hears of your workout. With the different sounds you maybe to figure out ways not to make them so loud, like putting a mat under your weights so when you set them down, they don't clunk. Simple changes can really decrease the noise of a workout.
HTH,
Kit