Choi's reaction was odd because there is absolutely no doubt she committed a penalty. A rather obvious penalty. She can't possibly think the application of a penalty was unfair. Maybe her score had something to do with it. With a 2-stroke penalty added, Choi was going to miss the cut. Rather than have an "M/C" on her record, she took a "WD" instead. (Does that choice affect how much money she gets? Anyone know?)
Also odd because the penalty was just so ... flagrant. Choi putted about a foot past the hole. Tap-in range. She quickly walked to the other side of the hole and placed a ballmarker on the left side of the ball. Then she quickly picked up her ball and reoriented the alignment marker, and placed the ball back on the green. But when she did, Choi moved the ball to the other side of the marker, about an inch. Obviously, a penalty.
Watch the video, it's crystal clear:
Was this an attempt to cheat? I don't think so. Partially because of the comments Judy Rankin makes near the end of the video about Choi's reputation on tour (it's good), but mostly because Choi goes through the chain of events so quickly that she appears to just be careless in what she's doing. Plus, what possible advantage does the maneuver get her? It's a tap-in.
Golf fans with long memories might recall in the past a couple golfers who pulled similar maneuvers, but did so on a regular basis (until they were caught) and moved their golf balls from behind the marker to in front of it, inching closer to the hole. Bob Toski on the PGA Tour in the 1950s, Jane Blalock on the LPGA Tour in the 1970s. Both claimed (and maintain to this day) they were not doing it consciously. But both were suspended. (Blalock eventually sued and won reinstatement.) Ironically, Toski was Blalock's instructor.
At any rate - whether you believe Toski and Blalock were consciously cheating or not - there doesn't appear to be any reason to accuse Choi of that. She was just careless.
The refusal to sign her scorecard and accept the penalty is weird.