Why does VIKI allow Dr. Calvin to fake Sonny's destruction? Since Sonny was independent of VIKI's control via the uplink, wouldn't it have been logical for VIKI to have Sonny destroyed?
VIKI didn't allow Calvin to fake Sonny's destruction, Calvin hid Sonny out of sight and grabbed a stock NS-5 (from her lab) to destroy in his place.
When the time came for the execution, she placed the fake NS-5 in the chair and injected him with nanites. The real Sonny was presumably one of the (apparently quiescent) robots hanging up in the background.
As far as VIKI is concerned, it would appear that Calvin doesn't have a view-strip on the wall of her lab, forcing her to rely on a webcam when she interacts with her boss. VIKI didn't know that she'd pulled the switcheroo because there aren't any cameras for her to use to see into the lab.