It's admirable that you're thinking of the welfare of your company and I can see how you would be wary of it impacting on your future career prospects but I believe you're actually in a strong position.
The biggest concern is in future recommendations. Most companies will be looking for confirmation that you did work for company X, that you were in position Y when you left and that you weren't sacked. Beyond that, the reference isn't all that important.
With that in mind, you need to think about what you want to do. Do you actually -want- to leave, or would you be happy to stay if things changed?
If the latter, it might be worth trying to rectify the situation. Your boss will (prbably) not want you to leave as it'll leave them short of resource and experience, plus look awfully bad on -their- record.
Go to them and lay your cards on the table. The best, and most professional, approach is to say "Our work relationship isn't good and it's got to the point where I'm looking to leave. We need to work out a compromise solution or I'm handing in my notice."
Give your boss time to handle this as some people, especially those who're lacking in experience and/or confidence, find it difficult to admit that they've made a mistake.
Whilst it's common practice for bosses to define what they expect from their employees, it's equally valid for employees to have requirements, too.
Bear in mind that the worst that can happen is that you change job. In today's climate, you should be expecting to change job occasionally, anyway. It's not always a pleasant experience but it's the way things are today.
You have power in this situation, don't be afraid to use it.