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Step 2. Instead, I have thought of storing the passphrase in a file (passphrase.dat.pgp), encrypted that file without password and passing the password to do the work using below command.

How exactly do you "encrypt that file without password"?

At any rate, this is probably a bad idea. Often the best way to proceed for scripting GnuPG tasks is to remove the passphrase from the certificate.

Step 3. To my wonder, when I execute Step 1 first and then Step 2 (within a short span), it works, but if I directly run Step 2 ( which actually will be happening as a part of solution), then it doesn't and fails for "No secret key" error.

This tells me that GnuPG is caching your passphrase with gpg-agent. When you run it the second time GnuPG sees the passphrase is in the cache and uses that, without ever needing to ask you for the passphrase.

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