Akai didn't have a choice. Kid blabbed to Bourbon that the luggage of the train was bombed, so Bourbon was going to move "Shiho" elsewhere. If Akai didn't act when he did, the situation might have changed and forced Kaitou Kid to use something Shiho wouldn't ever use -- like smoke bombs. That would ruin any plan Conan had to turn the Black Organization's plan against them and fake Shiho's death. (Personally, I think the train case was poorly done from a writing perspective. Conan acted too perfectly and certainly with the little info they learned on the fly IMHO. Conan's plan probably wouldn't have gone so well if more Org members were on the train, like Gin, or if the members weren't Bourbon and Vermouth. Besides, what if the Org's plan was to douse the whole train in sleeping gas, search room to room, and blame it on Kaitou Kid who was staking out the train for his next heist? If Conan was really behaving realistically, he wouldn't have let anyone board the train or done something to sabotage the departure before anyone could board. Letting Ran and the DB get into an unknown situation with murderous Org agents is pretty arrogant of Conan as it stands.)
It was much better for Akai to use his own face in that situation rather than Okiya's. If Okiya was seen then he might be traced to the Kudo household, putting Haibara and Conan in danger. If his face as Akai is seen, Kir might die, but Shiho and Conan would be okay because Akai could go back to disguising as Okiya. (I think Akai is prioritizing Shiho over Kir in part because of Akemi's promise.)