Ciao Jeremy, currently the ImageMosaic can handle fine raster where the grid-to-world transformation is scale and translate, hence now skew or rotation.
In light of this limitation I would suggest to perform a warp of your images upfront using, as an instance gdal_warp.
I have worked myself with Side Scan Sonar data in the past and I always used this approach even because otherwise at runtime it would be expensive to apply a very complex transformation just for visualizing/extracting. Btw, make sure to retile and add overviews properly.
I few useful links: http://goo.gl/74XUPq http://goo.gl/wdVjSd