Removing the auto aim gives the EM rifle a disadvantage over other sniper weapons at this point. Other weapons fire without a delay, so when the weapon is fired, players don't have to maintain their aim. The EM rifle also telegraphs its shot with the laser, letting your opponents know that the shot is coming. It requires even more skill than other weapons, making it less than a legendary weapon.
For many, especially in higher rank SP matches, EM rifles were an equalizer, helping to fend off other overpowered mechs and weapons, where now they're a liability. Some may think the changes balanced the game, but based on the responses on forums and through the in-game chat, it seems far more feel the opposite, and Plarium is choosing to listen to the few over the many, constantly trying to push a narrative that it was necessary, rather than accepting and owning that it was a mistake and that they are at fault. Almost every response to criticism about the changes I've seen from Plarium support has tinge of disdain and resentment toward players who don't agree with Plarium's decision.
The biggest issue is that a lot of players purchased the weapon and upgrades because of what it was, with the expectation that it would stay as such. If they are receiving so much backlash, then that should be a clear sign that any change wasn't welcome, and if Plarium intends to keep the changes, then they should be prepared to eat the cost and refund players who request for the cost of the EM rigle and upgrades in exchange for those players losing the weapon. I'm sure there are a lot of players who would accept losing their EM rifles at this point in exchange for the money they spent on it. The problem is that Plarium seems to have no intention of doing this, they made all the money they wanted on a weapon that they designed to be popular, then changed it to encourage players to purchase other weapons with no expectation to give players their money back.
Everything I've seen, it seems like Plarium's concern hasn't been game balance or players' satisfaction of the game, it's been making money. They made a quality, highly sought after weapon, that they would only sell. Once most people who would buy it did, they changed it to encourage players to buy other items, while refusing to refund any money. If them making the EM rifles as they were was mistake, then they should be prepared to lose the money they made off of it, if they aren't prepared to lose the money they made, then the way the weapon was wasn't a mistake, and didn't need to be changed.