I expect most (not all) .CR2 files to be importable by PhotoStructure v1.1.
Note that Canon uses .CR2 and .CR3 to represent a couple (!!) of different RAW formats. Version 1.1 of PhotoStructure uses dcraw, which only supports an older .CR2 format variant.
I updated PhotoStructure in version 2.1 and later to use a custom build of LibRaw, which should work for the newer Canon cameras.
If you want to try the alpha build of v2.1, that should resolve the issue.
I’m working through the bugs found in alpha before I release v2.1–please have current backups if you try an alpha (or beta!) build (but really, backups are always a good idea!)