What small farmers object to, by and large, is the manner in which this systems was adopted and the relatively severe nature of the burden upon small producers viv-a-vis factory operations...especially considering that the benefirt of the program accrues almost entirely to the latge packers.
(But, because the benefit accrues to large packers, they will compell some sort of tracking system sooner or later anyway)
Well, the other things is, most of the small-timers and hobbyists have a much better handle on where their animals come from and/or are going, simply due to the scale of operations.
Biosecurity is indeed an issue due to the potential of bioterrorism, and that is part of what NAIS is trying to address. However, NAIS is indeed overkill, especially for small producers (or subsistence types) because they are unlikely to be very inviting or effective targets.
I agree that a better, more cooperative (and less high-handed) process would bring about more participation.