"But as long as the trailer is attached its analogous to driving up hill both ways (continously)."
That depends on how long your "both ways" is going to be. In my case, it can be about 70 miles of pretty constant uphill, from near sea level to about 8500 ft. I do most of it in 3rd - the Insight is perfectly happy in that gear at freeway speeds.
So if you're going to be pulling a light trailer with a MT, just downshift

But the key word here is light. Honda, like most if not all automakers, puts a lot of things in its user manual for defensive reasons. When they say no trailers, they're aiming at the sort of person who'd try to tow a power boat or 30-foot camping trailer, then claim warranty repairs.
People need to use a little common sense. If the draw weight of the trailer is low enough that it can be towed behind a bike, you're probably going to be putting less load on the engine than you would putting the canoe on a roof rack, since that'd create mucho aerodynamic drag while a trailer would be in the Insight's wake.
Personally, the only thing that stops me from getting one for my sailboard and the kayak I wish I had is that I just haven't had time for sailboarding or kayaking lately
"You should install a clutch switch, this will disable IMA on hill climbs..."
Actually I should just get my MIMA install finished. Haven't had time for that, either, though maybe sometime this month.