Here's the answer I received from Ofcom regarding the Broadcasting Code. It's good enough on paper, but how it gets applied in practice is the key.
After confirming that "violence" in section 2 did include "sexual violence", despite a distinction being drawn between the two earlier in the document, I got this answer to my question on section 3.
The application of Rule 3.1 is essentially concerned with incitement, that is - very broadly speaking - the active encouragement of crime or disorder. Were a broadcaster to include material that actively encouraged or procured the commission of sexual offences it would be in breach of the rule. I think the prospect of such material being screened is remote.
Our application of the Code to the portrayal of sexual violence is strict. We recognise it as an especially sensitive area - from the point of view of offence as well as of harm (particularly in respect of its possible effect on those (few) men with violent sexual impulses towards women) - and regulate it accordingly.
From that answer it seems most likely that challenges to Ofcom regarding the screening of sexual violence portrayed as legitimate sexual behaviour are more likely to succeed under Rule 2.4 than Rule 3.1. I watch very little Ofcom-regulated broadcast material myself, so I expect that I won't personally be putting in any complaints - but if you do, drop a note in comments to say how it went.