There is a difference between control issues and confident pitching. As a kid is maturing as a pitcher, they should be taught (encouraged) to be aggressive. I know of pitchers (DD's team mates) at 14u who were afraid to throw an aggressive inside pitch. Their timidness developed over time out of fear that their coach would get upset and yank them if they hit the batter. What happened was that over time these pitchers developed a timid attitude towards "taking chances", which gradually eats away at self confidence. The subconscious is a powerful thing, and these pitchers got to a point where they couldn't throw inside "risky" pitches to save their life. They start throwing "safe" pitches which wind up in an outfield gap - or over the fence. "Safe" pitchers are also more apt to be injured by back-at-you hits that were not inside far enough - another reason to ignore the "just throw strikes" method.
Now, from a TEAM perspective, base runners are a punch in the gut, just like walks. Somehow, especially at the higher levels of the game, they nearly always come back and bite a team in the a**. So I can understand a coach wanting to limit free bases. So a coach must make a tough decision, and no two situations or teams are exactly alike. IMO, 14u is still a young pitcher, and development is paramount. You have to walk a fine line between not stifling development of a confident, fearless pitching style, and keeping a game under control - wins and losses. Again, no two teams are alike. I prefer to err on the side of letting the pitcher take some chances, and letting them know the "why and how" of those chances. If anything, they learn how important it is to practice things that help them with control issues. Then they won't be afraid to throw an inside chin-high rise ball in college. Pitchers MUST learn to be gutsy, and that comes from having the liberty (within limits) to take chances during their developmental years.
Another analogy - fouls in basketball. A high school player is allowed 5 fouls in a game. Those fouls have the potential to hurt the team if they are shooting fouls. BUT - there are MANY situations where a foul is a GOOD thing. Fouling a poor free throw shooter, stopping a fast break, etc. My point is that the word "FOUL" should not be taught as a negative to players, but rather as just a part of the game. The time and place determines if it's good or bad. IMO, a winning team with four fouls on every player is nearly a perfect game.
In the end, it's all about knowing your pitchers. WHY are they hitting multiple batters? Are they fearful of being aggressive, or do they simply have poor mechanics. An astute coach should always have a bench conversation after the fact so that the pitcher understand your reasoning. Remember - young kids are "trying to please" the adults, and getting yanked for violating a HBP rule smells of failure to a kid. Be sure to explain that HBP is part of the game, but it must be kept in perspective. A conversation about all the details will go a long way toward squelching fears of failure, and letting them know you expect them to work hard on control, mechanics - and inside pitches. Don't sugar coat a bad performance, but give them exact details about what they need to do to improve.