THE SOUTH RWYS (32L, 9R, & 4R) WERE BEING CTLD BY THE SOUTH LCL CTLR (SLC) & THE NORTH RWYS (9L & 4L) WERE CTLD BY THE NORTH LCL CTLR (NLC). AT 1543:26, SLC TOLD UNITED FLT 973 (BOEING 737) TO HOLD ON 32L & EXPECT A 3 MIN DELAY BFR TKOF. AIR WISCONSIN FLT 954 (FOKKER F27) HAD BGN A VISUAL APCH TO 9R. AT 1545:23, AFTER COORDG WITH NLC, SLC CLRD THE F27 TO CIRCLE (SIDE STEP) FOR A LNDG ON RWY 9L & CHG FREQ TO NLC. THE FINAL APCH PATH (EXTD CTRLN OF 9L) CROSSED OVR RWY 32L. AT 1546:53, SLC CLRD THE 737 TO TKOF. AT APRX V1 (133 KTS), THE 737 PLTS SAW THE F27 CONVERGING, AS IT WAS ABT TO CROSS THEIR INTENDED TKOF PATH. THE F27 CREW DID NOT SEE THE 737. THE 737 CAPT DID NOT THINK HE COULD SAFELY CROSS UNDER THE F27 OR ABORT THE TKOF. HE ELECTED TO AVOID THE F27 BY CLBG OVER THE OTR ACFT RATHER THAN PASSING UNDER IT. AFTER THIS INCIDENT, THE TWR PROCEDURE WAS CHGD SO THAT NO TKOF CLNC WOULD BE ISSUED TO A DEPG FLT ON RWY 32L UNTIL ARRIVING ACFT, CLRD TO LND ON RWY 9L, HAD REACHED THE THRESHOLD OF THAT RWY.