Option 1: Talk to your assembler and see if you could use two different temperature processes.
- Do the Lead-free profile first (that goes to a higher temperature)
- Then, after those parts are done, solder the leaded parts on with a leaded temperature profile.
This satisfies the requirements of both. (you don’t need to worry about stenciling as BGA’s have solder balls)
Install lead-free BGA’s with an IR rework station (which also supports temperature profiles). It is more difficult but possible.