Alfaro may get a pass b/c he's a catcher, if he hits with power and is plus defensively they can live with his warts.
Williams won't get that sort of free ride, too many OF prospects and free agents available to stick with a guy who wastes a key asset (speed) by not getting on base.
I think plate discipline is a combination of, yes, discipline, teaching yourself to take a pitch or two to gauge a pitcher's stuff, staying off high FBs no matter how tempting, etc., but also vision, if you can't pick up the spin on a baseball you're gonna get fooled by sliders all day. Smart hitters learn what they can hit, and will take a 3rd strike (hoping it's called a ball) if it's a pitch they know they're gonna hit .100 if they swing. Of course, if you can't hit a breaking ball, and struggle to handle a changeup, you're probably gonna have a short career in any case.
This trend toward running counts deeper started when Klentak took over, it'll be interesting to see how they draft in the future, my suspicion that most top 10 rd picks will be disciplined, while Klentak will take guys like Hall later and try to teach them how to work counts - if it's hard to teach, it makes sense to use your top resources on players who have that ability, and gamble with lower round picks on free swingers.
There's a good reason not to take disciplined hitters later, because the disciplined hitters with good bat speed won't be around, and the free swingers will have more upside than the disciplined hitters with average bat speed. I remember a number of disciplined minor league hitters (Esty for example) who looked good at lower levels but got exposed as they rose, much the same way junk ballers can look good in the low minors.