I think that replacing icon that way will force a heavy editing of configuration script. Maybe it could be done with bash script, which would be run from lime tools in the end of compilation - if target is LINUX, then run script which will relink an app with resource file.
BTW if You have WINE, on linux compilation should end with icon being replaced for windows target now (but You should have lime.ndll for Your linux architecture also so that script could run).