I think whether Guidance is fine or a problem depends on how the table uses ability checks.
At my table ability checks only happen when they are important, the outcome is in doubt, and there are consequences. There are no trivial ability checks as that takes interrupts the flow and tension of our game.
In each scene the players are asked what their character is doing. Then time passes and checks are made if they are warranted. So if a Cleric has Guidance they have the chance to cast it for one character, bit not all of them. As it is touch and only lasts a minute it might not even be possible to use it on certain characters. The Cleric would need to.be nearby.
I 100% agree with you. ...But... That assumes players are not metagaming, acting without outside knowledge, or your just restricting the Cleric to "pick one to help, because your all of doing your own things at the same time"
I think the issue the OP is having comes from the "you walk into a long hall way with 3 doors, one is open, what do you do?"
The Scout wants to look around the room (perception check?)
The Wizard wants to search the open room (investigation check?)
The Rogue wants to check one of the closed doors to see if its trapped and/or locked and work his way in.
The GM wants to let them all do their things and actually has something for them all but they all wait for the Cleric to walk around casting Guidance.
So wild he doesn't mind the extra 1d4 he seems to be getting annoyed with all action waiting for the Cleric. If there are not trivial checks and they are all acting at the same time then only one should get guidance, so... they all wait for the cleric to walk around one at a time. Sure, all the checks have an important none trivial check the GM prepared... but how do the players know that? Why do they all treat every check as important without knowing they are? When the rogue finds the door is trapped, he calls for the Cleric for guidance because he now knows he is in danger but why would the rest wait? If all checks are important the
players learn to wait because they know they would not get a role unless it was. So roll means I need guidance.
The characters don't know and would appear to be waiting for no reason and
that breaks immersion. That is the root of the OPs issue.
To me (and the OP can correct me if I am wrong) but the problem the OP is laying out is that the players are meta-gaming and breaking emersion for everyone to wait for Cleric Guidance spam because they are all desperate not to fail any important check that the characters would never know is important.