Alert, Locate, Evade, Counter, in that order. This matches my thinking pretty well.
For me, "Evade" is a much more useful description than "Run" (blindly). Especially since it follows "Alert" and "Locate".
Actually-and your misconception is quite common, the actions don't have to be done in any order. They're just in that order to help people remember them.
For example, if your alert is a guy coming through your door with a gun, you likely won't be trying to alert and inform the building of the attack and/or give a description and location of the attacker. (Typical actions that go with the A.L. and I.) You're likely going to go right to Evade and/or Counter.
The system is intended to be used as a guide. For example, someone in authority in the building announces on the PA that there is an attacker in the back hallway wearing all black and carrying a rifle. If you're in the front hallway, you can go straight to evade and evacuate. If you're in the back hallway, instead of running (especially blindly), you can initiate a lockdown. (And the program goes into a lot of details on how to secure a room from within.)
The training that comes with the program even instructs on when and how to conduct an unarmed counter against an armed attacker. This is where the system, in my view, is a complete and total failure. The creators of ALICE advise you to run away if you're alone, arguing that distance makes you a smaller target and, therefor, more difficult hit. To a person with no shooting experience, this gives a false sense of security. All of us know here, that, in the confines of an office or classroom, you can't get enough distance to make yourself harder to hit. Furthermore, they advise to counter by throwing objects at the attacker, to break his concnetration and ability to aim, making it less likely he will hit anyone. Lastly, if you have sufficient numbers and no other option, to rush the attacker, tackle him, and restrain him using at least one person to hold each appendage (1 each on each arm and leg) a 5th to hold the head down, and 6th on the torso. So yeah, six plus unarmed people are supposed to charge an armed attacker and tackle him.