Samsung Galaxy S3 Stuck at Samsung Logo, possible virus?
Odin mode is run in a very very early stage of phone boot - that's why you don't see the phone logo when entering Odin mode. The virus (if it really is the problem) will not have a chance to execute its malicious code because the bootloader isn't even running in Odin mode. 

So yes, you can safely Kies your way back to working condition, but sometimes you should use the specially created Odin program (Google it, I can't give links right now as I'm on a slow connection) to flash the firmware by yourself if Kies doesn't feel like working.

Just note that either way, you'll have to download 1+ GB of firmware.