(Disclaimer: As I have had no legal training parts of this post may be completely wrong from a legal perspective. If so feel free to correct me)
Having got involved with the FIDE Rules and Tournament Regulation Committee, one thing I've noticed is the difference between how players see the rules, and how arbiters see the rules. But let me explain.
Most criticism of the rules from players concern rules that are published. For example, the rule concerning forfeit time or the rules concerning insufficient material to mate (cf KN vKN controversies) attracted a lot of criticism from players. On the other hand, when the RTRC was meeting in Dresden, most of the concern from arbiters was about rules that were not written. Their big worry was that without a published rule they wouldn't know how to make a correct ruling.
Part of the latter problem is caused by the lack of published case law, or the acceptance of it. If we think of the FIDE Rules of Chess as statute law, to mimic a full blown legal system, there needs to be a repository of published case law. By that I mean somewhere where arbiters can look up decisions previously made by other senior or experienced arbiters, and use this decisions as a precedent to support their own decision making. And just as in a proper legal system, such decisions may be reviewed by a higher body (appeals panel or FIDE itself), resulting in a definitive ruling for that set of circumstances.
Here is an example of what I mean.
In the Radjabov v Smeets game at Corus this year (2009) there was an incident jut before the first time control. On his 39th move Radjabov moved a rook but in doing so knocked over Smeets' bishop. Radjabov then pressed his clock without returning the bishop to the correct square. Smeets immediately restarts Radjabov's clock, and asks him to replace the bishop. Radjabov presses his own clock, but by this stage has lost on time.
At the time the arbiters took a pragmatic approach of letting the players agree to a draw (as Radjabov claimed that Smeets acted illegally in speaking to him during the game), but that doesn't address the 'legal' position.
Geurt Gijssen was asked about it in his April 2009 Arbiters Notebook column. In his opinion he felt that Smeets had acted correctly under Article 7.3 of the rules of chess, and that Radjabov should have lost on time.
Given Gijssen's position as chair of RTRC, I would suggest that this opinion is now established precedent for situations of this kind, and therefore as an arbiter I would allow a player to act in the same way as Smeets (restarting the opponents clock), without sanction. And I would do so until either (a) the FIDE Laws of Chess are altered to deal with this situation in a different way or (b) a higher authority (the full RTRC, FIDE Presidential Board or FIDE General Assembly) offer an alternative ruling.