On height
-Haruhi probably appears to be shorter because of the art style that's used in the series (And allot of other anime for that matter).
The girls are drawn with an exaggeratedly petite figure. In this image, Haruhi' body measured shoulder to shoulder only 60% of Kyon's shoulder to shoulder length. So while the girls technically are smaller, the biggest difference isn't in height. Of course the body size of characters seems to be more of an artistic taste, so fanart tends to bring a sort of standardization.(And I have no idea why I think of these things...)
On kidnapping
Option 2 response
-While that kind of scenario is fun occasionally (Evil overlord forcing the Heroine into marriage), I'm a kind of guy who really likes the actual kidnapping. Thus not having the girls actually abducted in a cute/sexy out fit is a bit of a bummer. Though both the outfits they end up wearing can end up being sexy. I'm personally not quite big on the death threats aspect though. It's much more interesting IMHO for the captor to be able to force the Damsel into something rather than resorting to threats, it just seems to contradict the position of total dominance the captor is supposed to have. Like in the example you gave, the (female)Specialist kidnapper could loosen the bounds enough to strip and change outfits, rebind the girl, and add cosmetics. This would be highly ironic if done to Haruhi.
Option 1 response
-Gangs ups are fun
. It really helps subvert the problem that a regular mook by himself can't efficiently physically restrain a girl [I]without[/i] hurting her if the girl doesn't succumb to Standard female Grab area (To many things to cover, not enough hands). A couple of low level villain red shirts working together could probably get it done efficiently.
Though there's something a bit more personal with just having one extremely efficient kidnapper. It has an entirely different feel when the damsel has been dominated by just one kidnapper who totally pwn3d her. There's just this sort of cool professionalism of an individual who can quickly subdue a girl without hurting her, and then making off with her over the shoulder.
But yeah, if you don't go one of these two routes with a non KO or threat (using a weapon) based kidnapping, all you're left with is a more clumsy proloinged kidnapping or one where the damsel doesn't resist efficiently. The first can be fun, along with the second if it's in character for the damsel (It'd make sense for Mikuru, but not Haruhi).
Bondage sure is fun