I guess first and foremost I want to start out by pointing out that there is no rule, no punishable action for those who choose to shoot during the melee only time. I want to strictly point that out. Unless the player is showing poor sportsmanlike behavior in other ways, there is no reason for supporters to be calling votekicks on non-melee players. I mean that is kind of counter productive to the whole reason you are there in the first place

I have found that most people who are running with guns do so because they are unaware of the unwritten guideline that regulars are running with. So this begs the simple answer, "well I just told them 'Melee only!' and they didn't listen." This is something that I think is the biggest problem that comes out of telling someone "hey melee only!" It falls under the same syndrome of spamming someone to seed by doing nothing more than inviting them to game. If I am a random pubber who has just joined and read "hey, it's melee only!" my reaction would be "huh? I didn't just join a melee only server, what are you talking about?" and keep blasting away. I have found that in my experience that explaining the situation in more detail goes a LONG way to making people play ball with the rest of the server. This is why I always type out something like "hey, we try to melee only until 6v6" or "hey we typically keep it to melee only until we get 6v6 or so." This does 2 things, first a defined time frame of which melee only will end that has the added bonus of telling them that the reason why we are doing it is due to a lack of players. It also gets across the message in a non-hostile, non-accusatory manner which, if enforced, would be enforcing a non-server rule. It is a suggestion, not a commandment, and I have received more positive outcomes from making sure my messages are sent like this than I have ever seen with anyone else (myself included back in the day) just telling the newly joined to "melee only."
Now, say a person still does not wish to play ball and is shooting despite everyone's efforts to make sure they understand what is going on. Well as everyone should know, that is when the use of counter guns is not frowned upon. However, this is not the end of that problem. The problem occurs when the team with the shooty guy on it continues to play as if there is no shooty guy. More than once the presence of 1 shooty player can take a friendly game of melee only seeding and turn it into a frustrating game of "are we meleeing, what is going on, well he is shooting, and he isn't, screw this im leaving." But what is a player to do? Well it falls to everyone on the server to start acting a certain way that discourages the actions taken by the shooty player (this is where I am sure there will be the "discussion" part

On the flip side, it is up to the non-shooty team to target the shooter with extreme prejudice. What do I mean by that? I mean ignore everyone on the opposite team and go all out on the shooter. Everyone is just aiming at the shooter until he is dead, dead, dead, and dead again. Once he is out of the way, everyone goes back to melee and fun times continues. An important side note while doing this however is to make sure to keep telling him that the server is trying to keep it melee only until XvX. This again does 2 things, a) it keeps the disruption of the shooter to a minimum, and b) the shooter is either going to get a clue and stop shooting to which, problem solved; get frustrated and leave (which I know some of you are thinking HEY BUT THAT IS BAD, but remember that it is the shooter's choice to shoot and so it is also the server's choice to try to discourage that action because the action of one shooter can turn a whole server from having melee fun to not); or not influence them in anyway, in which case the same thing keeps going on until enough people have joined for guns, in which case the shooter's impact has been severely curtailed.
So the biggest problem to contend with is the fact that everyone has to play ball on both sides. Again, this is just my observations on what I have seen work the majority of the time to keep early melee only to melee only. If someone is just shooting, it does not mean that everyone has to go shooty shooty. And in the end if it does, oh well. But if you are like me and like your melee only time, this works pretty darn well. Just remember, it is all about communicating and communicating effectively.