The opportunity cost was in selecting the cantrip itself

Casters generally are very limited in their cantrip options (unless you're going for a big multiclass cantrip-focused character) and choosing guidance is it's own cost by not picking other either combat or utility cantrips.

Additionally, the ability check needs to be made within a minute. If the task is longer than that, then I don't think it would be unreasonable to rule that guidance wouldn't be helpful in that situation - but that is up to the DM and table to determine and discuss. The same goes for anything being asked of a character that is not happening visibly where someone with guidance would cast. If it's the same character, I see no issue with them doing it as a means to help them 'remember'.

I don't think guidance is overpowered, and it's doing it's exact role - the same with other cantrips whose cost remains an action to cast (which is also a cost.) And since a player opted to go for utility over combat, you generally should let that shine when it's time to shine. Otherwise, everyone just goes all-in on combat (which can be fine, depending on the table - but beware that you may inadvertently be 'teaching' them that combat is the solution to things.)

Disrupting game flow

I don't see casting spells as disrupting, but as part of whatever is going on. It is similar to the Help action in that another player/character must stop and say that they are helping or giving guidance. It also generally doesn't take very long and empowers the characters.