To load and save multispectral images (consisting of pairs of .hdr and .fla files), you could use the Scyllarus hyperspectral image processing toolbox. The MATLAB version of this toolbox is available for non-commercial use and can be downloaded from http://scyllarus.research.nicta.com.au/
The functions to look at are FLARead and FLAWrite under src/io. With these functions you can read from and write to the .fla format (ENVI-compatible), rather than any colour image format. Alternatively you can save the image to a .mat file but this option usually produces a much larger image.
