Not TNE as such, but several specific aspects of TNE - Virus snaps the disbelief suspenders,
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Further, with the Hard Times collapse, Virus was needlessly added.
I find this interesting as my own tastes generally run to the harder end (no psionics for me), but I don't find Virus grossly offensive, if you assume AI is possible at all - it certainly isn't blatantly unphysical, as jump drive is. If it isn't derailing the thread too much, care to expand?
On your 2nd point here, I always supposed Virus was introduced partly to knacker the other empires that weren't directly hit by Hard Times. Otherwise the other powers would just steamroller over the wreckage of the Imperium. As they did a bit in the Civil War period - the Vargr cutting Corridor and the Solomani piling in.
Extrapolating, without Virus, you maybe end up with a situation where Imperial humanity is largely under alien/foreign rule - dystopian maybe, but not post-apocalyptic.
Sounds quite cool in its own way.