Windows 7: Can I turn on system protection thru cmd? Windows is frozen.

I think that I have some "corrupt files" that were deleted after some auto updates were installed. This has created chaos in my windows. Normal mode windows locks up when booted, and now it is doing the same thing in safe mode. The only response I can get is in command.

I also tried sfc/scannow, and i cannot get past 49% after 3 tries.

I have run virus and malware scans when safe mode was working. All were clean.
I tried to do system restore from cmd and system protection is not there. Can I turn it on from cmd? Or do I need to do a full repair?

Any advice would be greatly appreciated.

2nd post today. sorry. Not computer savvy and trying to save one with your help.

Computer will eventually open to windows, but it immediately freezes. It initally worked in safe mode twice, but third time was not the charm. it now freezes as well.

I am now in cmd which is jibberish to me. I cannot complete a scannow thru cmd. It stops at 49%. So, I tried the verifynow and it completed with this note:
"Windows resource protection found integrity violations. Details are included in the CBS.log windir\Logs\CBS\CBS.Log." What does this mean? Can I fix this? Thanks in advance.

Have you tried running SFC from a Command Prompt booted from the Windows 7 install DVD? Tutorial by Brink here: SFC /SCANNOW : Run in Command Prompt at Boot

If you do not have a Windows 7 installation DVD, you can download a legal copy with SP1 integrated from here: Official Windows 7 SP1 ISO from Digital River.
Make sure you get the same version you have, Home Premium, Pro or Ultimate and 32 or 64 bit. Note that Basic or Starter is not available.

I recommend using ImgBurn at 4X speed (or the slowest available) to create the DVD from the downloaded .iso file.

Edit: Just had another thought. You should run chkdsk /r from a Command Prompt booted from the Windows 7 install DVD first in case there are any file system errors present. Then run sfc as indicated in the tutorial.