You could probably also have fixed this on the Amiga by renaming the Instal~1.lha file from Workbench, or maybe you could have used the option switch that turns off pattern matching in LhA.
I would have thought putting the file name in double quotes would work. It's been a long time since I copied something across from a PC using a floppy but I don't remember ever having problems with files with ~ in them (other than my own ability to recognise what the file was).