Could you add a permission to either allow players to use the /kit command or one to disable a player's ability to use the /kit command?

You rename the /kit command to something else and then give players a permission with that name.
For example
In the CONFIG file
"Kit chat command": "goodies",

In the DATA config
},
"kit": {
"Name": "goodies",
"Description": "Basic kit, use wisely you only get 20",
"RequiredPermission": "kits.goodies",
"MaximumUses": 20,
"RequiredAuth": 0