Even discounting building destroyers, doors require action from the player, in that they require locking and unlocking.
Building destroyers are a problem, but not an insurmountable one-- artifact hatches and doors are indestructible. Regular hatches are also indestructible from underneath.
If you're willing to accept the minimal interaction involved in unlocking a door or hatch, it is trivial to build an impervious entrance:
#####
#h
_/#\_ ->to fortress
#####
side view; _ is floor, # is wall, / and \ are ramps, h is hatch cover
Such a structure can be made three tiles wide to allow the passage of caravans, as desired. Building destroyers will be unable to destroy the hatches from the left side of the structure (untested in 34, but true in previous versions). Flyers will be unable to pass when the hatch is locked.
Use of an artifact quality door or hatch makes things simpler. (Again, untested in 34, but true in previous versions.)
In order to reduce the amount of interaction even further, one must rely on pressure plates. It's possible to make an entrance into your fortress that can only be traversed by civilians. First, you have to filter out building destroyers:
###
H -> to fortress
###
top view; H is an artifact quality hatch installed on the floor (there are probably other possiblities for furniture, but hatch covers are proven in previous versions); path is 3 wide to allow caravans
Building destroyers will congregate at the artifact hatch cover, trying to destroy it. For long term safety, you'll need a way to clear the area. Atom-smashing is a simple way to do this, as the BDs won't occupy the same tile as the hatch cover-- don't want to atom-smash your artifact! There are a number of other ways to clear the area though.
Next, you want to separate creatures that are too small to set off pressure plates and creatures that avoid traps. To do this, set up a fork like this:
#####
##d
^###
##h
#####
top view: / is ramp covered by hatch cover, h is hatch cover over empty space, d is door, ^ is pressure plate activated by civilians, all weights, linked to both hatch and door
Creatures that are trap avoid and small creatures will take the south path. Other creatures will be unable to. Route the trap avoid (bottom) path through a long bridge connected to a repeater, that drops trap avoids back outside (ie, onto a path that leads through your entrance again.) I believe that fliers will take the north path, but I'm not certain.
If you want a 3-tile wide version of this for caravans, I'm not sure about it, but it should be possible. (Can't use doors in threes, so you have to use ramps covered by hatches to get an instant path-opened-by-plate effect.)
Note that during this part of your entrance, you may lose a few pets, things like cats. Also, keep in mind that trap avoids may follow other critters through the lower paths. You can repeat this part of the path multiple times to reduce that risk.
Finally, you need to separate the civilians from the goblins. This is pretty much the same thing as above, only your pressure plate is NOT set to civilians trigger, and the south path is a valid path, whereas the north path goes through the same kind of repeating bridge setup.
Note that your creatures will have a route outdoors, but it probably won't be the same route they take to get inside. Expect them to get dropped by some repeating bridges on their way out. Also be careful of fliers with this setup. You can make flier proof versions, but they're more complicated-- you've got to change the repeating bridges to containment traps, then have a way to clear the containment of critters, and you need to prevent civilian access to the containment traps in attempts to path outside.
Anytime you start messing with civilians trigger pressure plates, you can start some pathing problems-- but these designs shouldn't be problematic, because every time civilian path is blocked, an alternate path is opened.
All of this is based on my experience with earlier versions, not with v34. I haven't done extensive testing with the effects of "civilians trigger" pressure plates on different kinds of critters. For instance, I remember merchants and diplomats being affected by "civilians trigger" plates, but I have no idea about how wagons are affected. Neither am I certain about how map "residents" (cave critters) are affected.
EDIT: Turns out that caravans won't go up a hatched ramp. (Actually, it's weird-- they'll go up a hatched ramp, so long as the CENTRAL ramp isn't hatched. Whatever.) So the prospect of a no-intervention-required, siege-proof map that allows caravans is out. But if you're willing to give up caravans, you can do it.