The only purpose to running things in safe mode is when the malware is stopping programs from running in regular mode. But then thats why rkill was made but sometimes that don't help either. However, when booting to safe mode most of the time the malware isn't loaded into memory and your malware/virus program won't catch it like it would in regular mode. So it's always best to run your programs in regular mode after you are able to run it in safe mode to remove the infection causing your programs not to work correctly in regular bootup mode.
Hopefully that explains it and if it don't just say so and I'll try to explain it better if I can.