I thought the rule was stupid when I first heard about it, and I’m still not sure I don’t think that, but as with the three-pitch minimum rule for relievers, I’m sure I’ll come around to being fine with it.
Re the strategy part, I don’t know that it will result in any change because (I assume) a runner is already leading off the maximum amount he can get away with on every pitch anyway. Not necessarily to set up a steal, but to shorten the distance to run so if a ball is hit, they increase their chances of being safe, if ever so slightly. (And baseball is nothing if not a game of ever-so-slightly.)
I can’t think of a situation where a runner is not leading off to his maximum, except in situations where he must protect his hold on first base in a game situation where losing that base would be much worse than gaining an extra base would benefit (e.g., down a run and two outs in the ninth). And in a case like that I can’t see him leading off an extra six or twelve or whatever inches after the second throw over because, again, the cost of getting picked off would be too great.
There might be guys early on doing what you say, but once a few of them get picked off for their foolishness, I would bet that would stop. So I see this as less an incentive to steal bases than it is to limit endless throws to first which, I agree with you, happens hardly ever anyway.