LOBs mean you are generating chances - and probably converting them too. If a team gets 15 baserunners a game, leaves 8 a game and hits into 1 double play ... THAT'S STILL SIX RUNS!!
Here is the thing - Francona was not against running - he was fervently against making outs. (also why the Red Sox are generally near the bottom in sacrifice bunts) When you have versions of prime Mueller, Ortiz, Ramirez, Pedroia, Youkilis, Varitek and more ... giving your big dogs a chance to do their jobs without risking additional outs is generally sensible. If you have base stealers, straight steals make sense. Hit and runs depend on the guys - because you are taking a decision out of the hitters' hands, and you are basically punting on the possibility of a 3-run homer.
Cleveland has a .281 team OBP so far. If they could (and did) run like the 1985 Cardinals - that ain't generating more runs. There is also no number of 3-run homers that can work around a team of Will Middlebrooks' statistically. Their issues are much more fundamental - and something which Francona has to just hope the guys hit their way out of.
Holding baserunners I had more of an issue with - although the general philosophy of the Sox I am basically in favor of. Stolen bases are a pain, but if you get the guy at the plate out, it doesn't matter. The cost-benefit of slide steps, extra concentration on the baserunner vs focusing on the guy more likely to deliver the damage (the hitter).