jharle, if you are still looking for the answer... When I copy the vc1 interlaced video with BDtoAVCHD or RipBot264 version 1.15.0, I copy save the video to insane quality. Like quality factor 10, and the copy the audio track directly with no conversion. (RipBot allows this if your output is mkv.) Then for Handbrake I have a standard 1080p profile I use. I modify that for 1080i by setting the deinterlace option to slowest. Because I kept the raw audio, there is no loss of quality in the audio. Generally in the final mkv I keep convert the audio to AAC and 160 kbps, and do a second track with the original audio pass through. Most of my devices will use the pass through audio, so it is the same as the original. No stuttering. The video seems to come out very clean as well, with no macro-blocking I can detect.
Another option that also works is Leawo's free video converter can convert interlaced vc1 without issues. It takes about 1/3 the time as doing a double conversion. When I play the videos side by side, both look to be identical quality. However, I'm still doing the dvdfab -> makemkv -> ribbot264 -> handbrake approach to convert my Torchwood blu-rays as I find the mkv files produced by Leowo's nearly twice as large and there is no pass through audio, just AAC stereo audio.