I'd imagine adding special marker keyframes during recording (just a special name would allow people to add and manipulate these during replay as well) for pause and resume and then having an option to automatically cut on these in the Replay Editor (and maybe also in https://bugs.replaymod.com/show_bug.cgi?id=54).
Fixed in *-2.2.0-b1 Allows pausing/resuming/starting/stopping the recording and automatically processes the markers when saving the replay. Also re-works the Replay Editor UI to be more powerful and (hopefully) easier to use but letting the use place such markers and then running the same post-processor on it.