Minato can at least teleport everyone to a safer place, but he might use a lot of chakra to do that, HOWEVER it is still better for the people to get away from Pain's attack because if they got hurt then I don't think they can survive so by taking them out of the village makes them easier to survive rather than Tsunade's strategies and Katsuya.
AND the question is, what can Minato do after sending a lot of people away from the village to a safe place when he used his chakra? I believe someone as Minato can still fight against Pain, but with Kushina and Kakashi there then I think they might take this chance against all of them, including when Guy is there.
Remember about this latest chapter? Minato, Kakashi, Lee, Gaara and Guy combo team was able to damage Madara.