IF you think this is a big deal... since the official scorer is a team employee, why not have the visiting team bring their official scorer along on the trip? If there's a significant discrepancy between their two tallies (more than one or two assists/rebounds), appeal to the league office.
I just have a hard time seeing this as a huge issue, since you know that so many of the teams (Dallas/Houston come to mind in particular) are VERY stats-oriented, you know that they're keeping track of "good" numbers themselves.
It's never going to be perfect, anyway; if you're looking to measure Rondo against CP3, as an example, you've also got to consider the systems that they're playing in and how that affects assist totals. Brevin Knight used to rack up huge assist numbers, but more because of the system he was playing in rather than his actually being a better-than-average player.
The numbers could be measured perfectly, but there's only so much precision you can have even with "perfect" measurement because of how different offensive sets work.