How would I stop this timer using a function in my module script?

You could try stopping a thread with a variable outside the function and using break to exit the loop like:

local module = {}
local stop_flag = false

function module:StartTimer(Time,Playback)
local timerThread = coroutine.wrap(function()
for i = Time, 0, -Playback  do
    if(stop_flag) then
        break
    end
    local minutes = math.floor(i/60)
    local seconds = math.floor(i%60)
    print(string.format("Time: %i:%.2i", minutes, seconds))
    wait(1)
end
end)
timerThread()
end

function module:StopTimer()
    stop_flag = true
end
return module             

If there you would call this thread multiple times then I suggest you pass each of them a BoolValue that would be instantiated somewhere in the workspace and getting rid of it at the end of the thread

Here is a sample of where you create a boolean flag in case you want to keep calling the function without it affecting each other, do note that you have to return the flag so you can pass it to the stop function:

local module = {}

function module:StartTimer(Time,Playback)
local stop_flag = Instance.new("BoolValue", workspace)
local timerThread = coroutine.wrap(function(stop_flag)
for i = Time, 0, -Playback  do
    if(stop_flag.Value) then
        break
    end
    local minutes = math.floor(i/60)
    local seconds = math.floor(i%60)
    print(string.format("Time: %i:%.2i", minutes, seconds))
    wait(1)
end
end)
timerThread(stop_flag)
return stop_flag
end

function module:StopTimer(stop_flag)
    stop_flag.Value = true
end
return module             

now to call the functions:

local sS = game:GetService("ServerStorage")
local Timer = require(sS:WaitForChild("ModuleScript"))

local flag1 = Timer:StartTimer(100,1)
local flag2 = Timer:StartTimer(100,1)
wait(5)
Timer:StopTimer(flag1)
Timer:StopTimer(flag2)