And now can you give ideas on how?
Look at the source code for the bootloader. When you understand EXACTLY what it is doing, you'll know what you need to change to read the hex file from the SD card and write it to flash.
Do not expect this to be a 20 minute job.
I had a good look at section 27 of the Atmel ATmega docs... is a bootloader necessary? They have provision to not use one though that involves loss of self-programming capability and maybe makes it easier to end up with a 28-pin brick.
Even without using a bootloader it appears that knowing what/how/why the bootloader does what it does should be necessary to do the job. PaulS made a very sensible reply there.