Dealing with poor management, lack of supervision, and the desire to move into a different field I am halfway through the 4th year of my PhD and I have grown to find that I dislike the direction of my dissertation and the project that I am working on. My supervisor is extremely absent as he is running another research group overseas (bigger budget there so he puts his time there). On our side, we have little to no post-docs, and those that are around are trying to use the students to publish more papers for themselves to get faculty positions.

I have found a distaste in my current project and research subject and hope to move to another one that I have found more interest in. I find it mentally taxing to work in this group, as there is no help from seniority and there is a complete lack of focus (for myself and for many other group members in my situation). I am thinking about leaving with an MSc and pursuing a PhD elsewhere, but I'm worried about two things:

1) Will the fact that I took 4 years and quit my PhD for a Masters look bad when applying to a different school? I think I have legitimate reasons but I'm not sure if that is enough.

2) I imagine my supervisor will not write me a good letter for wanting to leave to pursue other interests. 

Unfortunately I think this is a bit of a dilemma as I don't think I can graduate in 1.5 years (members in our group typically take 6 - 7 years), so stretching it would be hard. The lack of supervision, direction, and interest all make it hard for me to want to stay, despite my deep interest in research.
It almost goes without saying but still: it's really hard for internet strangers to correctly judge exactly how difficult this situation is for you. I'm answering just based on what you wrote and it's entirely possible I am missing the mark here. In that case, feel free to disregard my answer.

I'd be a bit wary to apply to a different school for a PhD now. It will indeed look bad on your application, you will need to get letters of recommendation from other people than your current supervisor, and you will essentially lose all the time you put into your PhD until now.

Your supervisor's absence and lack of local leadership is really demotivating. And it is easy to lose interest in your own research in such circumstances. Then again, research can at times be very demotivating and future research employers will want to see a certain tenacity in you dealing with demotivation. Giving up three years of research to go somewhere else does not show that tenacity.

Are there other options to explore? Can you move overseas with your supervisor? Can you start collaborating with a local professor, or find local trustworthy people to help you regain direction and interest? Is there any way you can involve your current supervisor more in your project?