If it's something potentially useful, I let it stay in hopes that some entrepreneur will reopen it. If it's yet another Canned Food factory or the 10th Cement plant, then I'm happy to see it go away, except that the stupid Capitalists in this game will then build ANOTHER Canned Food or Cement factory there. Talk about wasting money....there are 6 bankrupt Cement factories in the country, along with 3 subsidized ones that are all losing money.....so somehow, just because there's a 3-day spike in demand every 3-6 months, they think that building another is going to turn a profit?
Keeping the bankrupt factory there at least insures that they don't replace it with another of the exact same thing. It also serves as a placeholder for late-game high-tech factories. Once you research a couple of late-game techs (electronic equipment, automobiles, aircraft, fuel, etc.) then it's time to remove the bankrupt factory and place something more critical for the later stages of the game.