That is what I do, if there is something I want to assimilate, I turn AA off and run my cube over there. Once it hits the siege frigate with the assimilate ability, it then open fires on it and blows it up before it is complete. I have even tried to have it run away after the ability, but nothing.
That is a conundrum, since I turn off the auto attack. Next I give them a move order to anywhere in the area (just to properly clear out anything that it might have stored in it's command queue). Then I click the assimilate tab and manually tell them which ship to assimilate and everything goes fine for me (I just tested this method out and it works 100%).
Also Stress and Team, I am happy to see the new splash's for the loading screens. Having zero sins loading screens seems to make the mod feel better (I also liked the game Icon that you had in your previous versions and have kept it since).