Hello, I had this same issue and finally found something that worked, I hope it works for you.
I got a USB flash drive and went to another uninfected computer... actually it was a MAC and I downloaded
http://www.surfright.nl/en/downloads/ hitman pro trial to the drive
Every time I updated my Microsoft Security I had to go back and undo it because then I couldn't open it. same error you have
I put the USB in my infected computer and ran the proper version (mine was hitman pro 64 bit cloud trial)
It detected over 1100 issues and once I activated the free trial, it fixed and deleted the malware. I was then able to run the 39 updates to MSE and it still opened!!!!
Good Luck, someone from this community directed me to the Hitman, so thank you to them for that :)