I assume you mean the local charge up without a beam and then single fire shot, so I'll respond based on that assumption! I'm not the original designer on the Charge Rifle, so I can't comment with 100% certainty on the decision, but the main answer is counterplay and victim frustration.
One of the major axes of power for an Apex weapon is something I personally call "burstiness" (it's a technical term). While TTK and DPS refer to how quickly a weapon can kill someone, "burstiness" is how much damage is done in one short moment, or how _spikey_ it is. Most snipers have quite poor TTK, i.e. they don't down players as quickly as any of the other guns, because they have very slow fire rates comparatively. But, the tradeoff for this is that they do lots of damage in one shot, which has advantages in certain situations like catching someone by surprise, or engaging in peeking poke battles where players will hide back in cover as soon as they start taking damage (and you can hide in cover to protect yourself during the long time between shots). In general, those advantages are more meaningful at longer ranges where you are more likely to be hidden and players can't push on you from your poking position as easily. So what do players do when they are being shot by snipers, what's the counterplay? We try to provide this by utilizing Apex's exaggerated projectile ballistics -- projectiles are pretty slow and drop pretty significantly at range. Victims of snipers can jump, move erratically, use legend abilities, etc. to make it tough for the shooter to hit their target, especially while moving. There's also an element of trying to preserve some competitive integrity. When we make a sniper more bursty, say Kraber one shot headshots, we make the ballistics more difficult for the shooter -- the Kraber has very slow projectiles that drop very hard for a sniper. The hope is that if you get headshot by a Kraber from long range while running, there's at least the thought of "well that was a nice shot", knowing that hitting those shots is tough (this isn't perfect, and we are looking at potential Kraber counterplay improvements for the future).
So, on to the Charge Rifle. It has a low fire rate and high damage, so it has those "burstiness" advantages mentioned above. However, because it's a hitscan weapon, it circumvents a lot of those other weaknesses. It hits moving targets reliably, and it gets the reputation that it's much easier to use and hit people than other snipers. So, we needed to inject some unique weaknesses for the gun to make up for its unique strengths. The initial charge up beam helps with a lot of these issues! If you are in a peek battle, the victim knows when the big damage is about to come out and can take cover, reducing the peeking power. The initial beam helps victims time when the shot is going to come out, so they can try to do movements at the right time to dodge some of the damage. Also, by moving half of the damage to a sustained beam, we could do the swaying pattern, otherwise the Charge Rifle gets really quite strong in hipfire which was a bad time in playtests. With the titanfall charge rifle, the charge up waiting time is really only visible to the user, but not the victim. Being suddenly beamed with a huge damage spike that you can't really expect the timing of or dodge or see is pretty frustrating. When you can respawn 5 seconds later and folks are never that far away, it's not so bad, but in a BR it just feels bad.
The elephant in the room: the Charge Rifle was (and debatably is) still really frustrating on launch. I don't want to go too into it, but I'll give some high level thoughts on that. It wasn't super strong in terms of people getting kills with it, but it did restrict victims in a really harsh way that felt awful. Because of the strong ability to track moving targets, and because of the much wider more spread out cover in Worlds Edge (new map at the time), players could get "locked down" by Charge Rifle players. You could peek fight them to some degree, and you could beat them up close, but if you were stuck in a POI 100m away, the time it would take to run to another defensive point was just too long and they could reliably down you or do tons of damage. The weapon is very "sharp", it has impactful weaknesses and strengths, and it comes out relatively balanced in aggregate numbers; however, with how Apex plays, the "tracking moving targets" strength was too restrictive and frustrating to play against! This was in a time where we were trying to add more depth and viability to long range fighting in Apex, but sometimes things don't work out how we would like. Lessons learned, and it's always worth taking those risks to find the good stuff!