I presume the reason why ImageIntegration expects at least three images is that you can't do rejection with any fewer.
If you want to do the noise-weighted averaging without rejection you can "trick" ImageIntegration: just add the same files twice if you are dealing with FITS files. With XISF files there is some file locking that prevents this (you get an error when you run the process) but you can just make copies and add those.
Cheers,
Rick.