Then you are saying the same thing about Matt Cain, he was used in this fashion last season.
I've said this to you before. Last year was Lincecum's first year in the majors. Not only was it a learning experience for the major league staff on how to use him, but it was his first full professional season. So they cut his season a little short, both to save him and to try out others as starters. In addition, the season was lost at that point, nothing to be gained from starting him.
This is a new year. The arm strength to throw more innings was enabled by him pitching more last season, it should have prepared him to pitch a full season this year. They also have a season of handling him and now have a feel for what they can and cannot do with him. Plus, a year's experience dealing with Tim, knowing when to believe him and when not to, seeing when they should take him out, and so forth on his behavior.
If you say that they are harming him, then list some studies where this has been shown. BP has done some work in this, but I wouldn't say that their work is definitive yet. And most of the stuff you read on this is derived from BP's theories.
And at what point do you stop babying him? Would you continue to shut him down every year to protect him? Would you really do that if the team was competing for the division title?
And if the Giants go to a 6 man rotation when/if Lowry returns, they would be protecting the arms later in the season, when arms should be more tired, not now when their young arms should not be tired at all. Would that flip-flop your opinion then?
Everyone thinks Lincecum is invincible and some sort of cyborg, or something, but I didn't like him throw 120 pitches in a game.
So, I think Bochy left him in too long. I wouldn't have sent him back out after he was at 108 or whatever it was.
His college workload is often discussed when it comes to this sort of thing ("Well, he threw a ton of pitches in college") but college innings =! major league innings.