The obfuscated full-featured program will be downloadable from the web.
License will stipulate that it is freeware only if used in a non-commercial nature.
Should I worry that prospective acquirers will not consider buying over the software?
Will they think "There's no point acquiring the rights to it since crackers may reverse engineer it or prospective customers may just use it illegally"?
That being said, if that's your main concern then don't do it. Implement a trial period or ship demo version with limited functionality.