Here's the version that would be created via using choice A if instead of were replaced with rather than.
Judge Bonham denied a motion to allow members of the jury to go home at the end of each day rather than to confine them to a hotel.
The new version is still not correct, because there are a couple of issues.
For one thing, there is a tricky parallelism issue.
to allow almost seems parallel to to confine, but actually they are not parallel.
The to before allow is part of a motion to, while the to before confine is part of an infinitive, to confine. The second to is unnecessary.
A more correct contrast would be allow rather than confine.
Alternatively, the second to could be seen as indicating that the jurors are confining themselves, as if the meaning were the following. The jurors with be allowed to go home at the end of each day rather than to confine them to a hotel.
Either way, by removing the second to, one can create a more correct version, although even in this version who is doing the confining is maybe still slightly ambiguous, and the jurors could somehow be the ones doing the confining.
Judge Bonham denied a motion to allow members of the jury to go home at the end of each day rather than confine them to a hotel.
The construction using be confined in the version created using choice E solves that ambiguity problem, because that version clearly conveys that the motion is to allow the jurors to go home rather than be confined.
Judge Bonham denied a motion to allow members of the jury to go home at the end of each day rather than be confined to a hotel.
I am not sure which I like better actually, the corrected choice A version or the choice E version, but that's what's going on in this question, and the simple answer to your question is that simply replacing instead of with rather than in choice A would not make the choice A version correct.