Skip Sandra Goodin's missions. Yes, really.
I had thought this was the one obviously incorrect choice out of who to skip, but it turns out that if you meet Goodin for the first time after killing Menesch, she forgets her first 4 missions and skips to the "Protect Uhler" mission. (She also forgets to pay the bounty for killing Menesch, but I don't think we care.)
Tayla's missions contain some awkward choices regarding missile conservation and how to deal with the militia. I think the way to go here is to do one more Galaxy duping run at the start, kill all scripted-hostile militia rather than afterburning away, and then pay Roman Lynch's extortion fee after the final mission. All the "good-guy" factions then forget about our cop-killing spree, just in time for us to return to the civilized half of the sector. (Just like Goodin and Murphy, we don't need to go back to Tayla after her last mission to hear her say "well done".)
My route right now is to do the first Oxford mission, which lands you at Edom, then do 3 Lynn Murphy missions, which gets you to New Detroit. Then go to Pentonville, do all Tayla missions, and get the reputation reset at Pyrenees. This conveniently happens after killing all the scripted-hostile hunters I'm going to kill (apart from Menesch and Jones, but we can take the first hit and don't care about the second). When going after Menesch I go via Perry->Tingerhoff(refuel)->Nexus->Capella->Sherwood->Regallis. This dodges a load of scripted-hostiles because the game didn't expect us to go this way. So we also gain time from not having to talk down angry hunters.
I haven't broken any records doing this, but since I'm rustier than a second-hand Tarsus, that doesn't imply very much. This might be faster than the current route.