That's a really tough situation. So much respect for your commitment to pursuing the MD/PhD route in spite of it. I feel a little inadequate giving advice for something so complex, but I'll try.
I have heard rumors that schools don't want to invest in international applicants who they think have a good chance of finishing their training in the states and then going back to their home country. This is a perception that you might want to be mindful of—and it could impact the decision to let your visa expire and go back home. Please talk to other applicants/mentors who know the situation a little better for international applicants; I could be wrong. I just want to raise that point so you ask someone else about it.
I'm not sure what kind of school list you have on your mind, but if you're on SDN I'll assume you're going to be reaching pretty high. You need to perform well on the MCAT. That will make more of a difference in applications than putting in 70 vs 40 hours/week in the lab over the next four months.
That said, I think there's a nice middle ground you can get to, if your PI is open to it. If I were you, I would approach her and say something like 'I've delivered on XYZ. We're starting the manuscript now. I'd like to take a step back from the hours I've been working and just do 9-5 so that I can spend the rest of my time focusing on the MCAT and applications. Will you still support my visa anyway?' That's a very reasonable request IMO.
tl;dr I think that staying in the states and studying/applying would be the best plan.