"Don't use on a ship with more than 1 Agility" has always been suspect advice, and in the era of the Tractor Beam, it's actively bad advice.
A 2-Agility ship will roll 0 evades about 40% of the time.
A 2-Agility ship will roll 2 evades about 14% of the time.
That leaves 46% of the time a 2-Agility ship will roll exactly 1 evade.
Using C-3PO on a 2-Agility ship has always allowed flexibility: Do I want a guaranteed evade, or do I want "burst defense," either because I need it to survive or because it will be demoralizing to my opponent?
And C-3PO allows a 2-Agility ship to generate a 3-evade result, something that can be very important. Doing so is only 14% without a focus token, but it remains an option for when not generating three evades means destruction. And it is significantly easier to do when holding a focus token.
C-3PO on, say, the YT-2400 has always been a good choice of crew. It's never been a popular choice of crew, but those are different things.
Finally, C-3PO on a 2-Agility ship that's been hit by a Tractor Beam is, of course, C-3PO on a 1-Agility ship.
First time I ever get hit by a Tractor Beam, I'll let you know. 
As far I know, the "era of the Tractor Beam" hasn't begun, and we have little to fear from it. Era of the triple-scouts I'd give ya.
I guess I might agree that 3P0 on the 2400 isn't "bad", it's more that there are generally better choices available. In the math you've presented above, a guess of 1 (which seems to be your default unless imminent destruction demands otherwise) will be correct only 46%.
On a 1-agility ship, a guess of "0" will be correct 62.5% of the time. That's a significant increase in efficiency, making the 1-agility ship the right choice. In my opinion, of course. 