While you are correct that your particular lens should be turned off before manually focusing it, I think if you do this a lot you are going to be wearing the AF/MF switch out pretty fast... maybe you already have.
Instead, to accomplish the same result you can simply leave the AF turned on and point your camera and lens toward a distant object and activate AF by half-pressing the shutter release button. That will set the focus to infinity, which will also make the lens physically the shortest possible for storage. Same result without having to flip that switch so often.
Live View focusing isn't something I do enough to be able to advise about it.
One note of clarification: you are using what Canon calls "Quick Mode" or something like that, in Live View, where it momentarily drops down the camera's mirror, focuses, then raises the mirror again for Live View to be active.
That is not the "pentamirror" being dropped down and raised for Quick Mode. The pentamirror is part of the viewfinder assembly, above the mirror that you see inside the camera when the lens is removed, above the focus screen, inside the "hump" on the top of the camera. Rebel series cameras use a pentamirror (to save weight and cost) to reflect the image in the viewfinder, while the more advanced Canon cameras use a true pentaprism.
This is a relatively minor thing, but could cause confusion while discussing and trying to solve your problem.