The way I solved it was to open System Preferences → Keyboard → Application Shortcuts and override the shortcut for the Delete Conversation menu item.
Ultimately, I had both "Delete Conversation" and "Delete Conversation..." (note the "...") set to ⌥⇧⌘W (Option-Shift-Command-W). (When I set just one or the other, a mysterious second menu item would appear. Setting both solved the problem.)
Now ⌘⌫ (Command-Delete) works as expected, deleting to the start of the line.
Hope that helps.
Last edited by sharplet; 11-13-2012 at 08:23 PM.