No, Kirk didn't order that to prevent the ship from falling into enemy hands. He ordered it in the hopes they could destroy V'Ger before it reached Earth.
KIRK: Mister Scott, be prepared to execute Starfleet Order 2005.
SCOTTY: When, Sir?
KIRK: On my command.
SCOTTY: Aye, Sir.
ROSS: Why has the Captain ordered self-destruct, Sir?
SCOTTY: I would say, lass, because he thinks, he hopes, that when we go up, we'll take the intruder with us.
ROSS: Will we?
SCOTTY: When that much matter and anti-matter are brought together, oh yes, we will indeed.
And anyway, once again it was (effectively) a brand new ship with advanced tech, not an old junker.