Well that's all fine and dandy if everyone is having fun playing out in-party fights.How on earth would you stop them? Take away their character sheets and say "NO, you aren't allowed to do that!" That's bound to reduce irritation
If the players conflict with one another, then let them play out the conflict. You say it has no dramatic value, but I'd bet money it has far more dramatic value for those players then anything a DM could make.
I really don't get your reasoning for charm person being less offensive than a hit with a sword, I'd go as far to say that it was much more offensive, can you think of anything worse than someone having control of your mind?
Now, I've seen it ruled different from place to place, but out of curiosity, if the cleric made the saving throw, the spell itself was silent and required no motion, and the cleric didn't make a spellcraft check...how did he know someone tried to charm him in the first place?
Generally, the characters have already saved each other's lives more than once... and then they do something that annoys each other... and they immediately leap to violence.
"It's what my character would do!" is a lame excuse. Players choose who their characters are and what they do. Choosing a character who generates dissension is choosing to sow dissent.
"Yep, Bob, you were right, you WERE playing in character...but it's clear to me that THIS character you were playing was not a member of this PC team, but an NPC villain with other aims"
most of these yahoos in my experience are doing this to assert their superiority
Nope - not if it's wrecking people's fun.Is "It's what my character would do" an okay excuse for something most characters would do, like taking a swing at someone who insults their mother?
Problems like this might be avoided by a group template, something I first heard about on the feartheboot podcast . . .

(Dungeons & Dragons)
Rulebook featuring "high magic" options, including a host of new spells.