I am trying to get a paper published but it is joint with my supervisor, so I have to do it her way. At the moment I don't feel confident that I have the skills to submit a paper on my own.
I hope that your supervisor respects your differences, in an ideal world I think they should be able to see the value in something that is good but has a different approach to theirs, but it is a very personal thing.
I was advised that publishing during your PhD is a GOOD thing. My associate supervisor says that the examiners can "sometimes get confused between something that is bad and something they don't like", and that one or two publications in quality journals helps to clear it up.
Best of luck