The issue is. people bought the game here expecting free updates until the game no longer gets updating. Presumably the steam version will now get updates leaving anyone who purchased the game on itch.io in the dust with no new features while features will be added on steam. So it's less about people expecting it free on steam and more that they expect free updates on here when they know steam will get them. Even buckshot roulette still updated the itch.io version of the game AND the steam version.
It's a slap in the face for people who supported the game early on. You support the game to be told "ok no more update guys. You'll have to buy it a second time. My hands are tied!".
So I think it's perfectly understandable why people are upset about not getting steam version because they know that version will now be the only one getting updates and they no longer will get updates on itch.
Edit: I will say i do appreciate the discount. Even more so that you pointed out it was for mostly people who already had the game. I don't know if you sent emails out to the itch.io owners to tell them the game was released and is on offer. Regardless it is a nice gesture. I am just pointing out why people are upset. ,