You know, Matt, now that I think about it I kind of like that version better than skipping over the girl who is on base.
Suppose the CR already on base is your best hitter. If you skip her turn at-bat, the offense is being put at a disadvantage through no fault of their own. Simply replacing her with the next available CR seems to best fit the spirit and intent of the rule.
Rule 7-3 is in place to cover a batting-out-of-order violation. In that case, the offense has committed a violation of the rules and if their hitter is skipped they have put themselves in that position.
It will be interesting to see if NSA does address this as Mike has suggested.
The standard rules of softball covering line-ups, substitutions and re-entry ensure that dilemas like this can't happen. Here's another example of a quirk that can come up when you tinker with those standard rules:
Some leagues will use a continuous batting order, where you bat the entire line-up, instead of the standard nine. What do you do if a batter is at-bat, say the count is 2-2, and the batter is injured and cannot complete her at-bat?
Under standard rules, you put in a sub and the sub assumes the 2-2 count. With the CBO rule, technically there are no subs because everybody is already in the line-up!
You could simply skip the injured batter and send up the next one with a fresh 0-0 count. But that isn't fair to the pitcher who had maybe thrown some quality pitches and was on the verge of a strikeout. It also creates the loophole of a weaker hitter, maybe the last in the batting order, "faking" an injury and putting a better hitter, the lead-off-batter, at the plate.
You could have the next batter in the line-up step in and assume the count of the injured batter. But that isn't fair to the hitter who might come to the plate with two strikes already on her.
Another possibility is declaring the injured batter out, but that gives the defense an out that they didn't really earn.
Over the years I have seen different leagues that might handle this any of those three different ways. They each had anticipated this and written a league rule to cover it. Actually, two of the leagues didn't anticipate it at first, had this situation come up in a game and cause an argument, then wrote their rule after-the-fact.
And that is the worst case to have, similar to the NSA courtesy runner dilema- to have one of these odd-ball situations come up and not have a specific rule to cover it!