Can't think of a fool-proof way either, but I'd imagine this stuff produces fairly consistent laptimes and it won't send chat messages, which is a start.
If I understand you 'program' it by driving around and recording your inputs. A solution then would be to use the new add/remove objects packet in the next LFS version to randomly change the track layout in subtle ways. You could have a bunch of pre-designed layouts and randomly switch them every so often. That would mess them up quite a bit, and you could detect cars that frequently hit layout objects and make them, I dunno, do a captcha to prove they're human or something.
maybe LFS should report what InSim applications are connected to the client to the server, and if a new one connects - by the looks of it, it uses InSim, outSim and outGauge
If there are speed limits on the cruise server, perhaps changing them at few zones from time to time might discover such a bot. This would have to be used along with some other mechanisms like checking the consistency of laptimes and driving lines though...
If a bot like this is left running constantly on an online server then its going to mess up the lfs world most driven distance and laps charts? May not be a major problem but another reason why it should be stopped