Sounds... problematic, but there's potential in there.
A suggestion would make the SI a complete Gary Stu. He can dictate terms he's in no position to make to people that outrank him, is disrespectful to the chain of command and not only does he not get in trouble for doing so, but comes off as endearing for it, stuff like that.
Another thing would be making only Eila the perspective character. Shirley can be resistant to the SI influence, but not immune, and she too would eventually fall to it.
Eila herself is completely immune because of the nature of her powers: she thinks she can see the future, but she's actually reading the script a couple lines ahead of everyone else. And since the SI is a metanarrative aberration, she knows everything about him, his very existance, is wrong.
The SI will naturally try to seduce Eila, but she will rebuke him every time. As in most other Mary Sue/Gary Stu stories, any force to oppose their every whim will inevitably be the villain, and Eila will unfortunately be no different. She will become ostracized by the rest of the 501st. Their scorn, particularly Sanya's, will of course hurt her but it's still something she has to do because nobody else can.
The SI will start doing crazier and over-the-top stuff to seduce her but every time she'll tell him to fuck off. He will grow more desperate.
Eila didn't know at the time, but she stumbled on the only way to kill a perfect Mary Sue/Gary Stu: make them fail. The SI will then do something that will make the other witches realize he went too far and he will out himself as the monster he is. Cue a leadstorm, with Eila and Sanya putting the coup de grace.
The SI's death resets the timeline. He never existed, and the witches wake up to a normal day.
So yeah. A suggestion.>>2388966>another Strike Witches fanfiction cliche: the Axis of Time ripoff.
Tell me more. Never heard of this.