I wouldn't call myself a teacher, more like a fellow student, but I'll take the liberty of giving you my thoughts anyway.
1. 士道は今さらながら身を竦ませた。
The causative indicates the subject is causing the object to act, even here, where that means Shidou is making himself (his body, more specifically) act.
This seems like a normal way to say it.
1'. 士道は今さらながら身を竦めた。
This is almost the same thing, but more directly, using the transitive 竦める instead of 竦む. I feel like this places less emphasis on the effort that the subject is exerting, but I don't think the difference is big.
2. 士道は今さらながら身を竦まらせた。
This means the same as 1. but using 竦まる instead. The dictionary define 竦まる as meaning 竦む, but 竦む is, I think, much more common. Especially in this conjugation.
3. 士道は今さらながら身が竦んだ。
4. 士道は今さらながら身が竦まった。
This sounds like Shidou's body is recoiling by itself, without his volition. Again, 竦む and 竦まる are the same meaning, so aside from the common vs. the uncommon word, there's not much difference.
Sentences 1 & 2 do make me consider more strongly the 2nd definition of 竦む, as if Shidou might be 'cowering' or 'shrinking in fear'. Sentences 3 & 4 since they suggest a lack of volition strongly imply definition 1, that Shidou must have frozen stiff on the spot.
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