Well, to be honest, I have no sympathy for people who put lunatic things like quotes in their file names.
I also assumed that quotes weren't allowed in filenames, and I maintain that sane people don't use them even if their OS allows them to.
If you ask me, Windows shouldn't allow accented characters in filenames, either, and I don't particularly mind that the aligner fails on such files.

That said, you are probably right. One issue is that different versions of the various OSes work differently in different circumstances and I don't want to make bold assumptions. E.g. XP seems to always use double quotes, Vista doesn't even allow drag & drop into the console... I'm not sure what Win7 does. For all I know, it might use quotes only if there is a space or other escape-worthy character in the file path. At least one major OS (Ubuntu, I think) does this. I.e. you get /folder/test_file.txt but '/folder/test file.txt'. So the code could easily break if a newer/older OS version works differently or you didn't test thoroughly enough.
Researching all these permutations seemed like too much trouble for the few crazies who use impossible filenames.