|I wouldn't do that, you will just be making problems for yourself. If you must connect a fan to a molex connector, get a proper adaptor. They are easily avalable and not expensive.|
I would find out why the system is not recognising the fan when it is plugged into it's correct sokcet. There may be two or more connections on the motherboard that will take a three pin fan, but only one of them is for the CPU fan.
Most BIOS software these days will shut down the system if it connot recognise a working CPU in order to protect the CPU. Connected to a molex connetor or a connection not meant for the CPU fan it wont be able to.