That's actually her Reasonable Authority Figurehood shining through. Chiffon has observed Satellizer for long enough to know that she doesn't respond well to any attempts to bludgeon her into submission.
Instead, Chiffon tries to, y'know, reason with her. "This is a violation of school regulations. Cease and desist, please." The cowering is mostly there to make it clear to Satellizer that Chiffon neither intends nor wishes to fight her.
And it works. Satellizer responds much better to people who nicely ask her to stop.
- This isn't so much Wild Mass Guessing as "plain and simple truth."
- Rapidly becoming a much more credible theory, due to the E-Pandora transforming into ACTUAL NOVAS, and the heavy implication that Chiffon was one step from going Nova herself. After all, while Nova invasions certainly are treated as a big deal and cause a moderate amount of casualties among the Pandoras, given the kind of hyper-destructive weaponry the Novas seem to possess, they appear to cause remarkably few civilian casualties and destruction. A rapidly ascending fan theory is that the Novas are simply the evil threat that the government dusts off every now and then to justify keeping total control over the civilian population. (Is that a trope? It seems like it should be) The reason the Nova invasions are getting more and more frequent is that the population is losing faith due to EXTREMELY questionable actions by the government.
- Jossed The Nova are shown targeting heavily populated areas and if the Pandoras don't stop them, they self-destruct IN those areas for massive damage and loss of civilian life. It's only once they find Maria's corpse that they begin targeting Pandora.
- Jossed Maria appeared before him and apparently warned him about the oncoming threat.
- Jossed In the Busters arc the Nova's "voice" is shown emanating from another dimension/galaxy, proving that Gengo did not create them.
Satellizer has Kazuha's stigma, and Kazuya is being hinted at as something more than human in some cases. The Baptism has been teased between the two of them for so long, it's impossible for it to not be something extreme either way. Either the Baptism itself will cause some unforeseen catastrophe that threatens to annihilate the world, or it will be pivotal in stopping a world-ending threat that's already in progress.
- Considering just how often the author uses Mood Killer on Satellizer and Kazuya every time they try to get intimate, it may not even be a "baptism" that brings about the end of the world. Heck, just them "knocking boots" may be enough to trigger Armageddon.