There is no such thing as amateur competition anymore, just eligible and non-eligible.
Plushenko "broke the rules" (i.e., pissed people off) when he didn't go to World's but skated in shows instead. If he had just not done the shows, he could have skipped World's no problem. (Rochette almost had the same problem, but managed to get clearance before the shows.)
The ISU thinks if you are well enough to skate in shows, you are well enough to skate in competition. But shows put so much less stress on an injured (or emotionally stressed, in Rochette's case) performer. I think it's perfectly plausible that a skater isn't in form for World's, but can still be in shows.