For me I like throwing story at those that wish to break the system and go all out in this maner. Think about what the reaction of people around him would be. Cops would Harris the group even on the simplist of tasks. People in normal locations would make it hard for the team to be inconspequously accomplish even a meet with the Johnson. Certain establishments that have policies against weapons would not let him in. Life would be rough and people would fear him. In oth words the teams public awareness will start to rise rapidly.
In the shadows everyone would know of him, he's the crome jock that can't get the job done with attracting too much attention. Fixers and others wouldn't hire him or his team for most missions as the inability to blend or get past scanners makes the team a liability to the mission more than asset. In oth words the teams notoriety will start to rise rapidly, especially if he uses brute force to overcome obstacles that cold have been circumvented with subtler means in a normal team. If the team doesn't get hired you can start having them pay one or two months expenses before each run and if you are not already limit their pay on runs giving bonuses to negotiation rolls to the Johnson, since he has to hire a team that can't understand the concept of covert.
All in all I don't think combat should be removed, but in a world as presented by Shadowrun covert mission should be common as Johnson's don't want to be known, that's why they use an alias. Dock the team pay if the do something overt in a mission.
All of this does wo things, it's takes the amount of combat down in your game giving your players more to do since the combat monster would hog the spotlight otherwise, and it makes your players start to put pressure on the player that is causing the problem as everyone is now affected by his decisions.
Once they fEel this pressure make the character an offer to join a merc company or become the bodyguard for a fixer in the game. If the players have been money starved, are pressuring the player and they are having problems getting jobs done smoothly he will jump at the offer and you can write him out on and have the player make up a new character.
No matter what though keep your world consistent and somewhat realistic and these types of problems usually fizzle out on their own, and players will also tend to shy away from these situations.
Just my 2 cents,
Red