RemoteTech Flight Computer and Realism Overhaul

[Epox75]

Hello everyone! I'm having a little issue when I execute maneuvers with the RemoteTech Flight Computer in Realism overhaul. Most of the engines are unthrottleable and they can be only cut off, so when the Flight Computer ends the maneuver it tries to throttle down but the engine of course doesn't stop. So I was wondering is there any workaround for this problem? 

Not using RemoteTech is not an option

Thank you in advance!

[Streetwind]

If you know by roughly how much RT overshoots, then you can simply assign that much less dV. That's what for example Scott Manley did in his latest series. His probes would reliably overshoot by 0.4 m/s, so he just plotted his maneuver nodes with 0.4 m/s less than required.