I think it makes sense to cap out the reputation at 4k on a beta site, to keep the "earned level" the same (even though the value is different).
That sounds crazy when you say it out loud. And for good reason. 4K is not "the same" as 20K, any more than 4 apples are the same as 20 apples.
Reputation is not directly comparable across sites, and never has been. That's true regardless of the privilege levels, beta status, presence or absence of ChrisF...
What is true across all sites is that after 20K, you can't earn any more privileges just by earning reputation. You have access to all the rep-based tools, and if you care to use them you can gain experience with them.
Yes, on beta sites you'll hit that threshold at a lower rep level. Heck, on private beta sites, you'll hit it even faster - at 2K, the same rep level that lets you edit on graduated sites!
But 20K is a safe value. Regardless of whether you spent time on the site during the private beta period, public beta period, graduated period, or some as-yet unannounced unlabeled gamma period, if you have 20K or more you're guaranteed to have maxed out the rep-based privileges.
There's a more important aspect to this though: the cap itself. Right now, the total score is evenly-balanced between reputation and other activity on the site; if we lowered the cap, we'd either be massively undervaluing reputation (by contributing at most 4 points to the total) or massively overvaluing it by contributing 20 points for 4K - you see, unlike the privilege thresholds, badge criteria don't change from beta to graduation; it takes the same number of flags to earn Marshal or reviews to earn Steward on Gardening as it does on Stack Overflow.
Most critically though, this doesn't matter. Your candidate score on a graduated site has no bearing on the score calculated for you on a beta site; you're up against folks who've been participating on the same site, writing about the same topic, with more or less the same voting patterns. If you've earned 4K and they've earned 20K, they probably contributed a lot more than you did. The goal of the candidate score was to prevent one form of participation from completely dominating the others, not to remove reputation from consideration entirely. On some sites, there may not be any candidates who max out all the stats - not enough reputation, not enough reviews, not enough things to flag, whatever. And that's ok! You're all still playing on the same field, with the same opportunities and challenges; the score offers a quick way to compare stats before considering more nuanced aspects of style and personality.