It's designed to be able to, but you will probably not be able to control the pump speed. It would be best to separate them. Pump on CPU-Header and Splitter with other fans on Sys_fan header. There are some minor differences (i.e. 3.3v line) between Sata and molex but for this application no. They will both provide the +12v that the fans require.
Did your molex splitter have a PWM cable to connect to your MB and was it connected to a 4 pin PWM connector on the MB?
Did your molex splitter have a PWM cable to connect to your MB and was it connected to a 4 pin PWM connector on the MB?