How do you deactivate this when you're not clicking?

First off, your code is a mess lol. I highly recommend using anonymous functions so that you can nest events inside each other. It will look a lot nicer and be more organized:

tool.Equipped:connect(function(mouse)

	mouse.Button1Down:connect(function()
		--click
	end)

	mouse.Button1Up:connect(function()
		--unclick
	end)

end)

Anyways, the reason your code never stops is that you never tell it to stop. On line 12, you start an infinite loop. It's gonna keep running no matter what.

I'll show you a pretty easy method in order to get around this. Create a variable. When a player clicks, make it true. When a player unclicks, make it false. Then create an infinite loop outside the events, checking what the variable equals and running code based on that.

local clicked = false

tool.Equipped:connect(function(mouse)

	mouse.Button1Down:connect(function()
		clicked = true
	end)

	mouse.Button1Up:connect(function()
		clicked = false
	end)

end)

while wait(0.1) do
	if clicked then
		--code
	end
end