Usage of は over に to mark seasonal changes

In this context, saying 葉が秋は赤いです instead of 秋は赤いです is not correct, because the 葉 has been already introduced in the discourse (i.e., it's "the leaf", not "a leaf"). If you really want to say 葉 twice, you can do so using は:

(The/This) leaf is red in autumn.

• この葉は秋には赤いです。
• 秋には葉は赤いです。
• この葉は秋は赤いです。(acceptable but slightly questionable: see below)

Note that you can have two は's in a sentence when one of them is contrastive. The は after 秋 has a contrastive function (i.e., 秋 vs 夏), which is important in this context. 秋は and 秋には are usually interchangeable, but in a case like this where two は-marked arguments coexist, it's better to be explicit and say 秋には.

If the subject was included, would the phrase look like "葉が秋は赤いです"?

It depends on what you want to focus, but if I had to naturally add the subject in this context, I'd make it topic:

この葉は秋は赤いです。

Don't worry, は can be used as many times as needed in a sentence whenever the context fits, for example:

このビルは南側は11月はストーブをつけるほどは寒くはならないです。

is completely probable when their focus in conversation at that moment is the (un)evenness of the building's insulation by season.

葉が秋は赤いです。

would be valid too if you don't intend to make 葉 as the ongoing topic. Then かえで (which has whole-part relation with 葉) would become the implicit topic, so that the full form is:

かえでは葉が秋は赤いです。

This option would be natural if your story develops like:

「かえで」の葉です。葉が秋は赤いです。赤くならなければ違う木です。

Would it be correct and maintain the same meaning if に was used instead?
Would it be correct to use には instead too?

に conceptualizes the time as a point, but adjective means a lasting state. 秋に赤い would mean "be permanently red at the moment of autumn", which explains why it sounds bad when you mark duration of adjective with に. Using は is a steady choice because it's like saying "be permanently red as long as (it is) autumn".

A verb (that implies change) will accept に, so that you can say 秋に赤くなります "redden in autumn".

i think you should use には for what you mean if you use に　you should use 赤くなる