I still think B & B killed Trip off in an act of petty rage against the fans for not sticking with the show.
"Killed our brilliant show? Well, we'll get you all! We'll kill off your most popular character! There! FU! Try bringing it back after we're gone! NO TRIP! MUHAHAHAAAA!"
I believe that is how it went down.
But I still think the way Phlox looks at Archer as Trip is going into the fix-it tube is very telling and seems to point to a massive plot underway. As in, The Good That Men Do.