The rule, as it stood last year, gives you plenty of options - 4 for the positive terminal, 2 for the negative terminal.
I certainly applaud your efforts to separate your wire colors for 12/24V... just do it within the confines of the rule
There's nothing wrong with using red and black for 12V, and white and blue for 24V, for example. It's within the rules, and it gives you the separation you want. For my team, we haven't used pneumatics since our first year. As a result, we've standardized our wire colors around gauges, so it's obvious what gauge the wire is at a glance.
This rule hasn't changed for a very long time, and I doubt you'll see it change much in the future. As you pointed out, industry applications have their standards and codes, why shouldn't FIRST have its standards as well? As an inspector, I can tell you that having standardized wire colors makes things MUCH easier when helping out any team at the competition. It allows us to unplug things, swap components, etc without worrying about what that particular team's "standard" is - we follow the FIRST standard and everything works out fine.