Yes, but the idea was that Bisharp can still take on Jirachi just fine even if Jirachi is trying to paraflinch it.
Why does there have to be a perfect answer to a pokemon for it to stay in OU? This metagame is not about either having an answer to something or not, it's about what decisions you make so that your team is more or less prepared for each threat. In other words, it's not a binary "are you prepared for X threat yes/no," it's more like a continuum of preparedness. As
Agent Gibbs put it, "the era of being able to run universal counters to the metagame's top offensive threats is long gone."
Moreover, the pokemon I suggested (Garchomp, Char X/Y, Bisharp...) are good for much more than just hitting Jirachi. You wouldn't be carrying "a cleric on top of a counter to handle one pokemon," you'd be carrying two good pokemon that just so happen to help out against Jirachi, as well as with other things. The goal is to make a team where all the pokemon work together, rather than individually each focused solely on their own threats, to minimize the amount of things that the overall team is weak against.
So no, you don't have to bring a cleric if making room for it would detriment the rest of your team. But if you find your team is weak to Jirachi and in your experience Jirachi is common enough to warrant preparation, then you might need to think about what changes you could make so that your team loses as little other coverage/synergy as possible while gaining some coverage vs. Jirachi.
By the way, only keeping things in OU that have perfect single-mon counters would actually exacerbate your complaints about the game becoming matchup dependent. That is how RPS works, after all. Rock is a perfect counter to scissors, scissors is a perfect counter to paper, paper is a perfect counter to rock.
I get the whole universal thing, that is what I actually used to believe before all of these bans started coming out over the last few months. Some of the Megas got banned because there was "little to 0 counter play" to them (Even though a Gengar with Will-o-Wisp pretty much shuts down Kang). The things that get banned can do what they do almost regardless of who they are up against. And then thigns that raise evasion are also banned because they also "take the skill out of the game" and turns it into "50/50's". In this case, Flinching is 60% and Paralysis is 25% for a total of 85%, which is worse than a the evasion you get from Minimize (brings you from 100% to 60%). That is worse than 50/50, that is 15/85 unless your pokemon is immune to paralysis, in that case it is still 40/60 chance of you succeeding on moving that turn (the equivalent of using Minimize). How is that competitive if Jirachi's whole entire strategy is the equivalent of evasion items/boosting? It's almost worse because at least if they use evasion, you can still boost your own pokemon, lay hazards, blow them away, or use one of the many moves that don't miss or have been tweaked in order to counter evasion.
Out of what you listed, against a 0 HP 0 Def Jirachi
Bisharp does 82.6 - 97.3% with SP
Mega Gyarados does 79.5 - 94.1% with EQ
Mega Pinser does 72.7 - 86.2% with EQ
Gengar does 76.2 - 90.3% with SB
Heatran does 63.9 - 75.6% with Lava Plume
Skarmory just leaves you on the defensive and will get paralyzed
Mega Manetric does 59.2 - 69.7% with Flamethrower
All of this is IF you get pass paralysis/flinch and are fast enough to strike first. Even then it still has Leftovers + Protect + Wish and the option to switch out after happily paralyzing you for free. Frail pokemon like Gengar become nearly useless when paralyzed.
Excadrill, Garchomp, Landorus, Rotom-W H sound like the only viable counters to Jirachi. Everything else, will get paralyzed on the switch which allows the Jirachi user to keep the momentum by switching out to something that will use your switch as a free turn to set up.
The main question I have and don't get is why this thing hasn't been suspect tested if it uses a similar strategy to evasion and can always get off a paralysis on the switch, while being bulky and fast enough to hit first and survive most SE attacks? It also forces many switches unless you already have one of the checks out. Where is the counter play or skill if my only hope is to carry one of the 5 pokemon (Mega Man too) I just listed or hope I don't get immobilized for 2 turns in a row so i can take it out? Isn't that the definition of 50/50 match ups? Also most teams already carry at least 1 of those 5 pokemon I listed, which is great for them, but for the rest of us it means changing our teams to follow exact same teams and strategies as everyone else, doesn't that make things stale?
TLDR -
It forces witches while Paralyzing anything that isn't Immune
Is faster than most of it's Counters/Checks and bulky enough to survive one hit without EV investment from most of them
Flinch turns games into 40/60 (equivalent of Minimize)
Paraflinch turns games into 15/85 (worse than Maxed Evasion)
It does the job of Support (Wish+Thunderwave), Stall (Protect+Paraflinch), and a bulky Physical Attacker with one moveset.