This sounds awful. Your poor dd. 
However, she has been let down by the school (very, very badly if she is coming home with bruises resulting from non-accidental injuries). The school, including the leadership, has let her down, so why would you want her to stay at the school, just in Reception? If the school has been unable to act on these very serious issues, then it will happen again in other year groups.
In your situation, I would move her and I would do it asap. I would start calling round other local schools to see where there are places.
As you say, the phonics check doesn't matter in the grand scheme of things, but your dd's safety and wellbeing absolutely does.
You say that you think that she may not have been ready to start school and this is why she is behind. However, I would hazard a guess that she would have coped fine and would be doing absolutely fine if the school had done a half decent job of addressing the issues you have mentioned. It is not necessarily the case that she wasn't or isn't ready for year 1.
Press the eject button if you can, don't just move her down a year. The problems won't go away.