Will try to answer both in one way .
If by that time , Miranda still didn´t trust Shepard , her character would demand to be on final group of Shepard party.
So basically even if you haven´t taken Miranda with you on the final mission part of suicide .
She would be contacted by TIM to prevent you from blowing up the base .
If she really was that Ceberus dedicated , she would have done it anyway .
You are talking about genetic perfected human being , with cold hard calculations .
And no mercy to put a bullet in somebody backside . or use her biotecs.
Now basically Miranda I have no doubt she will be a perma Squad member or Perma Crew member.
Cause basically the voice actress is too lovely

if Jack is back , so will Miranda .
Anyway she has the XO job , so she is safe to be on normandy Perma .
It is the poor people without a job lol , like zaeed ,grunt , kasumi , legion , thane .. that you cannot put them as perma ship members , So welldone Bioware in messing that up