Hi, good luck on your MD/PhD applications. I need some clarification though, are asking:
a) if you are are admitted to MD/PhD and THEN decide you want the PhD only, could you stay in your thesis lab to complete your degree? If this is the case, typically you'd have completed the first 2 years of medical school and then yes, you could just stay and complete your PhD if you've already started it.
if you are asking if you want to do a PhD instead of applying to MD/PhD and want to make the lab you're currently working in your thesis lab, then yes you'll still have to apply to the PhD program, rotate through labs and then hopefully the lab you're working in would pick you as a graduate student to do your thesis there.
Sorry if I misunderstood your question, but I hope that helps!