I look at it this way. Runs Scored are a "symptom" of getting on base, and Runs Batted In are a "symptom" of hitting for power, generally speaking. So, if I wanted to replace R and RBI with stats that are more lineup-independent, I would replace them with a getting-on-base stat and a hitting-for-power stat respectively. So, perhaps BB in place of R (especially good since walks aren't already accounted for), and Total Bases, or Slugging Percentage, or Extra Base Hits in place of RBI (actually, I would love to see Isolated Power more widely available as a roto stat, since it doesn't include singles as TB and SLG do).
One approach, as has been suggested, is to simply replace AVG with OBP, but although I love OBP as a stat in general, for roto purposes I would rather just add BB as a category to supplement AVG. Hitting for average and drawing walks are two different "tools," as it were, and isolating different tools is the spirit of roto scoring, as I see it. That's why I don't like OPS as a roto stat: even though it's a good measure of a hitter's overall ability, it's just too comprehensive, and as such makes most of the other categories redundant. In roto, get as many different "tools" represented as possible (which is why I'm a big fan of adding BB as a category), but keep them separate as best you can. Just my two cents.