Use of moda imperativo

I’m sorry that you (sing.,inf) are sick. Get well soon!
is translated as:
Lamento que tu estejas doente. As melhoras!

why is imperativo mode of estar used here? Why not estás?

It’s the subjunctive tense which is being used here. The imperative mood does fall under the subjunctive though.

W Wishes
E Emotions
I Imperative (Commands)
R Requests
D Doubt

The sentence you’re asking about falls under E for Emotions. Lamento que. Lamento meaning sorry in the sense of sympathy.

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@mhalai, like @reececox2000 said, it’s the subjunctive that’s being used here, more specifically, the present subjunctive. I’ll just add that although the subjunctive can also be used in an imperative sense, we do have a separate imperative mood with specific verb conjugations for the 2nd person singular and plural.