"If Microsoft forced either SmartScreen OR AppLocker"
Meh, just add a button or clickable link that allows the sysadmin to swiftly disable such warnings. Just make sure to put a scary-enough disclaimer that doing so can expose you to very bad, malicious stuff, from ill-intentioned people. It might get more application publishers to implement signing, just as Vista and 7 got rid of the "run everything as administrator" mentality through the use of UAC warnings.