で can be used also in a passive sentence.
e.g.
彼と魔法省とで、偽の口実が仕組まれた。
In the sentence above, the subject is 口実. That's why I used "agent". (As you can see, で can be replaced with によって in a passive sentence.)
The meaning is basically the same as が (except such like the passive ones, of course), but が could sometimes sound "strong" comparing to で. The grammatical difference is that this で is only used for an organization/group, as in the dictionary, or a side of two or more different groups/persons. で is originally from "particle に + particle て", and the nuance is close to において "at". Probably that's why this に is used only for these specific cases.
e.g.
その案件は私の方で報告しておきます。(= その案件は私が報告しておきます。)
(In fact, 私の方で sounds softer than 私が, therefore this kind of expression is often preferred in business scene.)
As for the difference between は and が, 気象庁は is the topic, as you know. This sentence is about 気象庁.
みんなで is usually categorized as "state". みんなで means "all together", but みんなが can mean "you all(except me/us)" depending on the context.
5 動作・作用の行われる状態を表す。「みんな―研究する」「笑顔―あいさつする」