First one doesn't say it would take thousands of years for the universe to be destroyed. Also, second one doesn't say the universe is destroyed.
What is there to explain? Even if the first panel said it would take thousands of years to destroy the universe, nothing in the second one contradicts that. It's just a really big goddamned universe with beyond countless worlds. If he destroyed three entire galaxies, it would still be "entire galaxies." There's a lot more to do than that.
First panel's thousand years, by the way, refers to the life span of Grandpa and the statement that Goku would be given a lot longer lifespan to go fight Majin Buu. Not that he needs 1000 years to fight him, he'll either win or lose in...I dunno, one or two?