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You won't have to wait long for the Red 9, so you may as well stick it out with the Punisher, rather than waste money buying the regular handgun back. Though if you have a save from just before selling the HG, reload that, keep the HG, claim your free Punisher and sell it right back to the merchant.
I usually just keep the handgun until the free punisher, then sell the handgun, then use the punisher for a little while until the red9 becomes available. I never upgrade the handgun, usually I throw all my money into the rifle since i'm playing pro and I know i'll have it until the end of the game.