Ya, everything you just said assumes you're charging at the castle facing Alexius directly, and thus he can use time magic to just win the fight.
If you simply use "a subtle and crafty approach", which is EXACTLY what you do in the mission, then Alexius doesn't have the time to use the time magic spell and you can beat him. Literally what you do in the game is the exact way to beat Alexius.
No way you spin this, is it a good idea to ignore the time magic once you learn about it. If you however never go to Redcliffe, or even to the chantry to speak to Dorion, then you're good. (Although then the issue is raised as why doesn't Coryepshit just get Alexius to stop you from helping the Templars.)
No. I assume nothing. Let me lay this out for you from my Herald's perspective.
Jonathan Trevelyan: So we are going to trust Dorian, Alexius' former apprentice, to dispel whatever barrier Alexius has protecting the castle and sneak Leliana and the scouts inside through a secret passage that might have been sealed since a decade ago or might be guarded now. If that is successful and if the scouts find their way to our location in enough time to help us, then we are going to somehow overpower a magister who uses time magic. We will do all this before Alexius can use the time magic to either kill me or go back in time, in which case he'll be able to make new plans to counter our strategy. Do I have that about right?
Leliana: Yep.
Jonathan Trevelyan: ... How about no? Here's what I do if I'm Alexius. *Eh-hem* "Mu hu haw haw haw haw haaa! Inquisition! Welcome to DIE!" Bzzzt, time magic. I'm dead. But let's say for the sake of argument that Alexius doesn't kill me immediately and he feels the need to strike up a bit of small talk, and lets say you and the scouts make it to our location in time to help us. Now I, as Alexius, say, "Good plan Herald, having Dorian sneak your scouts in like that. I'll remember to take measures against it after I go back in time." Bzzzt, time magic. Now everyone in that timeline is erased, Alexius goes back in time, and Dorian and the scouts get a giant rock dropped on their heads as soon as they enter the castle. Then I walk before Alexius unaware that anything happened to you until Alexius tells me so himself, then he proceeds to kill me instantly.
Leliana: ...
So... have we received word from Lord Abernache yet Josephine?
My Herald didn't actually say all this in my headcanon, but you get the concept. Okay, back to your points. You say the plan is to beat Alexius before he uses time magic, and yet he was able to cast it within two seconds because that's what he was prepared to do. So in essence, you fail. And besides, what you're suggesting is foolhardy because you assume that the Herald will be able to stop Alexius from using time magic. You have no way of knowing if you'll be able to pull that off. You are literally risking everything on the unknown.
Now, to answer your excellent question about Alexius using time magic to stop you from getting the templars. First, let's leave Corypheus out of it, since it's actually more plausible that Alexius would act on his own rather than waste time asking Corypheus for help. Plus, it's more likely that Corypheus was still recovering/traveling to get into position, and thus could not be reached. So let's say going to the templars forces Alexius to use time magic to go back in time and stop you. We must look at what options Alexius would have available to him in this case. He has only a few options, and the first step is to select a proper time.
He can't go back to before he took the mages, because he has to take the mages and get them on his side. Otherwise, it's him vs. the Inquisition and the rebel mages. So the earliest point is probably when you meet in the tavern, since he knows you are going to travel there. Like I said before, if he attacks you in this setting then it proves him the aggressor and you are justified in taking him down right there. It would be a risky move for him. If he were to bring all his men and have them lie in wait, then it might work. BUT, he could do this anyway if you approach him in Redcliffe Castle. So this possibility exists either way. All you can do is hope that your pre-Gull and the Lantern party is able to survive whatever forces Alexius had at his disposal at the time. And also remember that the Inquisition sent scouts ahead of your party to meet with Fiona. When you cross the main gate outside the village a scout informs you of this. So, if Alexius were to set a trap in this timeframe your scouts would have discovered it before you got there. Most likely.
So what other timeframes could Alexius have used? Another is the point in which you leave Haven to go to Therinfal. But in this case you can be prepared for anything. In other words, you can take precautions to watch out for any signs of Alexius trying to stop you. In this case you actually have defensive measures that you can employ, and you have a much larger compliment of guards to assist you and your noble allies. From Alexius' perspective, this is also risky, as he is basically only going back in time insofar that he can attack you in the present. He doesn't know how things will go. You are on an even playing field in this case, whereas in Redcliffe Castle you are on Alexius' turf.
The second thing to consider is what allies Alexius has in order to stop you. He can't mobilize the mages against you at The Gull and the Lantern because the mages would not have listened to him. The deal was to protect the mages from combat and get them to Tevinter. So commanding them to attack the Inquisition when they have made no hostile moves would seriously hinder Alexius' efforts in conscripting the mages. This would be true if he were to attack you on the road to Therinfal or at Therinfal as well. So he would only have his own Venatori forces, which were still undercover at the time. He might be able to attack you while at Therinfal, but then he would risk being attacked by the templars. And if he appears at Therinfal, then you must face him. So what? That's what you would have done had you gone for the mages. So it was inevitable. Still, at least this way you are on even ground, and perhaps have templars on your side to help you. Also, a larger compliment of your own troops.
He can't attack you after Therinfal, because conceivably you would have convinced the templars to your side.
So, by thinking the situation through logically, any Herald can deduce that going after the templars carries minimal risk. One could also conclude that if Alexius were going to use time magic to kill or capture you before the trap, then he would have done it already. Logically, the trap IS his way of killing or capturing you. So best to avoid it.