The task of changing a NH-28 is one of multiple reasons;
1: Due to the Black Spiral's control of at least one NH-28 unit, such a procedure may be put into use.
2: In case of enemy capture of an inactive NH-28 unit, which is then put into use to serve an enemy of the Empire.
3: In case of introduction of 3rd party manufactured NH-28 units, such as PNUgen.
4: Because nothing should ever be immune to everything.
------------
As for the technical issues... I did state that there were massive requirements behind capturing a NH-28 in a combat situation. As for a surprise attack, I think I covered everything... air speed and temp manipulation to prevent nodal support usage (The buggers don't work well in bad weather), temperature reduction to slow hemosynthetics... and other such cautions. Hrm, but with the addition of the notes on preventing power from reaching the NH-28's generator, it should also cover the CFS issue.
Anyway, during the early stages of the process, only an idiot would go near her without a power armor.
Also, the task of breaking the humans and nekos aboard the ship is a given, of course its going to have to be done, but it would also be nice to salvage the NH-28 unit. Such an expensive and useful killing machine should be given a chance to continue to contribute to the Empire, even if she is a pet or a sentient individual whom is given privileges if she behaves.
I think it is worthwhile to spend a few hours of IC time within an IC week to reprogram a machine which could contribute positively to a plot environment... it would also provide some interesting RP for whomever is playing the NH-28, and the trainers.