It's somewhat pointless to discuss if they're "scared" or not at this point, but the absence of the Neo at E3 isn't proof of your argument. Sony confirmed several days ago that the Neo exists, and that it wouldn't be making an appearance at E3 (presumably because they want to avoid it eating away at the PS4's current sales).
Regardless, it will be interesting to see how the Neo vs Scorpio stuff turns out. If the final Neo does reflect what we currently know, and the Scorpio has a similar advantage over it as the PS4 currently has over the X1, then it'd make for a fun shift in roles. It likely wouldn't have the same PR impact as the current dynamic did (since the lack of a Kinect would let Sony properly capitalize on the benefits of lower-spec hardware, and MS's shift to an Xbox+W10 combo makes the higher end hardware slightly less relevant), but it'd be interesting none the less.