Interfacing a chip which isn't soldered to a board is hard.
You can try and find a socket adapter for your package and build a programming rig yourself where you insert those chips. Those no-solder sockets can get very pricey depending on the package. (for example Loranger offers quite a few) In that rig you can program them using JTAG, which should be faster than a minute (depends on the flash size obviously). You have to take care with the layout to allow high speed JTAG access.
Another option (but sounds like that is not possible) is to program the chips with a needle adapter on the board via JTAG. You have to expose the JTAG pins with testpoints on the board to be able to do that. We typically use this approach and program the boards during our after-assembly-testrun.
Another option is to get someone else to do it for you: Send your chips to a professional programming service along with your software and get them programmed there.