1. First, the ctfmon.exe file 'isn't being detected,' but something which has been loaded into memory by the ctfmon process, which is why when you upload ctfmon to virustotal you don't get any detection.
The custom memory scan is the most thorough of the memory scans and it digs deep which can have unforeseen consequences. My mention of the scanning of memory, is a throw back to the old days when memory scans were very much the norm. The idea now is to prevent any malware getting into your system in the first place.
If there were a true virus on your system and it had loaded something into memory, there are likely to be other issues, somehow killing the memory block (as it isn't a physical file) would have little effect as whatever placed it there would be able to put it right back.
2. You don't in relation to ctfmon as it isn't ctfmon which is being detected, but a block of memory loaded by it.
