If you have to enter something into the console to improve runs then it should be banned.
This is a pretty stupid metric to determine if something should be banned or not. You could argue that having access to fullbright on shitty dark maps would give you an advantage. Clearly Pitchdown/up is the only real issue here and since it's a client command you can't really do much about it since the server shouldn't be able to see what you have it set to.
However bshear mentioned that his new plugin (or some other plugin I can't remember exactly) could see what clients have commands set to. With this you could possibly use it to check if cl_pitchdown/up has been changed from default (89 for both) and then use that to invalidate runs. Another solution could be to disable it on a map/server level. I am fairly sure that there is a plugin that could force commands to be executed by the client.
If this is possible you could have the client execute the following commands:
cl_pitchdown 89; cl_pitchup 89; alias cl_pitchdown; alias cl_pitchup
This would set pitchdown/up to their default values and then prevent people from changing them from these, I think this would be the best solution overall since it would remove the main issue (pitchdown/up) but not interfere with anything else. The only real issue with this is execution. Ideally it would be executed when you join Tempus servers since as far as I know there is no reason for players to have a different cl_pitchup/down value and if they did they would just need to relaunch TF2 and not join a Tempus server.
If a server cannot execute these commands easily it could always be done on a map level using a trigger_multiple (presumably at the start/spawnpoint of the map) and a point_clientcommand to do the same thing but obviously this would be somewhat pointless because as far as I know most maps likely will not have this.
Even if this stuff all happens there's still the issues of people who abused it before the rule was formally implemented. It's not exactly fair to punish them for something that wasn't against the rules when they did it but it would also allow times that are better than they should be to exist. The best solution would probably involve admins reviewing the runs and determining if they used pitchdown/up or not. Obviously this isn't the best solution because it'd only really make sense for them to review WR times because how time consuming it would be.