I honestly don't see how an argument can be made that his mechanics are off because he's too strong.
His first bad start was before the ASB - and he had "normal" rest prior to that time, meaning he should not have been stronger for that start.
Also, as someone else said, even without high pitch counts, the extra 8 warm-up pitches per inning, extra ABs and his running of the bases as a batter, etc. are all reasons for his IP to be watched early on and, again, are things that show he should be weaker, not stronger at this point.
Lastly, when someone gets tired, they lose form - not gain it. And too many times I've heard announcers (former pitchers) state that when a pitcher gets tired, he leaves his pitches up in the zone because he has trouble finishing off a pitch - which would lead to more flyblls.
So, IMO, Willis has a unique wind-up and is susceptible to having those mechanics break down should he get tired. This break-down would cause him to not get on top of his pitches, leaving them up in the zone. This is my guess as to what is happening now.
Can he fix it? I don't know. Maybe some extra rest, a few games where he's pulled after 80 pitches, some work in the video room or something can allow him to regain his mechanics, and therefore his sink, before the end of the year. I surely wouldn't drop him right now, though maybe putting him on the bench for a start in a hitter's ballpark might be in order until he shows he's fixed it.