Here's my take, FWIW;
From what I can tell, the only complaint seems to be that the alt key has been remapped from its previous role to a different mapping. So, while the functionality hasn't been actually removed, it ended up messing with the ingrained muscle memory for the function - and in twitch games and semi-repetitive strategies both, muscle memory is Kind Of A King. And since it's incredibly handy to for spotting enemies in visually noisy areas, for some players, it gets used a lot. Also, the switch from a single key to a two-key combo makes it more inconvenient, but that might just be me.
And as for the actual unit tagging feature itself, while I haven't really formed a definite opinion yet, I'm firmly in the "if you don't like it, don't use it" camp.
So, as far as I can tell, the simplest and least intrusive way of resolving this would be to map alt back to its default behaviour, and use ctrl-alt for the unit tagging.
Another option might be to merge both features and have alt highlight both unit directions as well as the marked units - at a quick look, it doesn't seem like they conflict with each other.
And finally, there might be the option of defining a hotkey for each option in settings, but that would probably mean implementation of modifier keys for keybinds, which may or may not be worth the trouble overall.
That's basically my view on the situation.