It doesn't really matter if you kill rot. (it should be mostly killed anyways) Personally, I would turn off the normal or anti-normal autopilot in any case. Time warping with an AP on isn't usually good.
AlignPlanes MFD assumes that all burns are done at full throttle, and the "engage Thrust" and "Kill Thrust" signs aren't meant to be followed perfectly. If you still have a few tenth's of a degree of RInc, you can often continue burning until RInc is zero. Just keep an eye on the closure rate, as long as it shows a negative number you can continue to burn.
Also, the "kill thrust" refers to the main engines, not the rotational RCS, so hitting killrot isn't needed.
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