You can run any software you want on your devices without Apple caring at all. Either your company is an enterprise licensee, or you pay your $99. Big deal.
$99 keeps the script kiddies out-- you know the ones who download iOS betas to show their friends and then complain that they managed to brick their device?
$99 keeps the script kiddies out? Excuse me? I've been running software written by "script kiddies" for my entire life, to great success. It's very likely that you have too. So has the rest of the world. Most of the internet runs on software written by those meddling "script kiddies".
That computer you've got your hands in front of right now? You need to spend $99 to run a web browser on it. You also need to write the web browser yourself.
Keeps those pesky script kiddies out, you see.