Supposedly not, although nothing is every completely balanced. The SWTOR developers want the story elements to be free though. They don't want people to feel pressured to play the story a certain way in order to be acceptable to Operations groups, so if there is a difference it will be small and shrinking with patches.
Side note: It has been stated that it is possible to do some extreme things, like kill or drive off a companion. If you did that you would lose access to a companion, which makes playing the game a little harder. But they did say that they wouldn't surprise you with it. If you're doing it it will be made clear to you that that's what's happening, and only people dedicated to that action for some reason will do it.
So, basically, you can make it a little tougher on yourself, but not accidentally, and in general the different choices should be balanced in the long run.