How do I make lazers not kill you when it disappears?

Make sure you are using a server script and not a local script. You cannot run a loop and wait for another part of code to run at the same time. The loop will continue to run and wont be able to check to see if it was touched. Use a stepped function instead, using increments per second as a basis to fade in and out.

function onTouch(part)
	print(part)
	local humanoid = part.Parent:FindFirstChild("Humanoid")
	if humanoid == nil then
		humanoid = part.Parent.Parent:FindFirstChild("Humanoid")
	end
	if script.Parent.Transparency <= 0 then
		if (humanoid ~= nil) then
			humanoid:TakeDamage(100)
		end
	end
end

local RunService = game:GetService("RunService")

local RATE_PER_SECOND = .5

local fadein = false
local waittime = 0
RunService.Stepped:Connect(function(time, step)
	local increment = RATE_PER_SECOND * step
	if fadein == false then
		script.Parent.Transparency = script.Parent.Transparency + increment
		if script.Parent.Transparency >= 1 then
			waittime = waittime + increment 
			if waittime >= .5 then -- Adds .5 every second, so if you want to wait 1 second wait till .5, 2 seconds woulkd be waittime >= 1. 1.5 seconds would be waittime >= .75
				fadein = true
				waittime = 0
			end
		end
	else
		script.Parent.Transparency = script.Parent.Transparency - increment
		if script.Parent.Transparency <= 0 then
			waittime = waittime + increment
			if waittime >= .5 then
				fadein = false
				waittime = 0
			end
		end
	end
end)

script.Parent.Touched:Connect(onTouch)