Alright, I was about to answerd this but Fey caught me.
Overall it's just this part.
the AI just draw an imaginarie rectangle around all the buildings owner of that AI; I am talking only about the Harkonnen ones, here the smuggler and Atreides doesn't count. As you can see, the player it's inside the area the AI it's about to defend, it believes that you are attacking it because you are "near" his base; that's the logic the AI uses and, because of that, he will try to fight you with any units available.
The best you can do it's what suggest Fey: 1 of those two bases, instead using the "harkonnen" side; change it into other side; Imperial, for example.
Then, on the missions settings change the alloc. index of the Emperor to be Harkonnen and that's it: of course later you need to update the Imperial AI tab, but at this point I guess you know how to do that (or you can just simply export/import the one the Harkonnen are using to have those two Ais to behave the same).
With that it's enough; with the "first attack building delay" you can control the time the AI waits until attacking for the first time. The bigger the number it's, the more time the wait to attack the first time.
Remember that 1500 ticks = 1 minute (in game time); so if you want that AI to wait 15 minutes before attacking the first time, his first attack building delay needs to be 15*1500 = 22500 ticks.