I would switch it off. Never seen a tripod that is adversly affected by IS being turned off.
Many people turn it off and that is, I think, the way to go.
I never removed mine though and I don't see any inconvenience on having it, other than the sound it makes. By this, I mean I don't see any big difference on recorded footages.
Remove it if you use an internal microphone.
I keep mine, because am switching between handheld, tripod and monopod; mainly on a monopod and the IS helps alot.
If you intend to use your DSLR alot for video; equip yourself with an external microphone and a loop.The hood helps stabilize during handholding, helps as well avoid initial vibration when you remove the DSLR from the monopod to handheld in the midle of recording. It helps as well when you have a wooden floor that causes microvibration when somoeone is walking by or when someone inadvertently bumbs into the tripod. On a monopod, the hoodloop is a must and my IS is always on. Actually, my favorite lens is 200mmL but it doesn't have IS so I switch always to the 100mmL. That makes this lens my most valuable.
As far as aperture, it depends on many factors. The aperture is mainly dicated by the depth of field that you want to achieve. 2.8 is minimum for 100mm. Most of the times, I shoot at 3.5 to 5.6 for sharpness. I shoot only 1.2 or 2.0 when indoor, during wedding reception for example, due to lack of light, and that has to be full body.
Usually, I shoot at 1/80th s, unless the light is too much then I shortens it to 160th or 320th then I use a filter.
You should be ok if you shoot at F16 outdoor. Indoor, you have to play with high ISO.